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ABCDEFGHIJKLMNOPQRSTUVWXYZAAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZBABBBCBDBE
1
Gephe IDGene-GephebaseUsernameGeneric Gene NameUniProtKB_IDUniProtKB_SpeciesStringSequence SimilaritiesSynonymsGO MolecularGO CellularGO BiologicalGenBankIDTrait CategoryTraitState AState BTaxon A IDLatin Name ACommon Name ARank ATaxon A LineageA=InfraspeciesTaxon A DescriptionTaxon B IDLatin Name BCommon Name BRank BTaxon B LineageB=InfraspeciesTaxon B DescriptionAncestral StateTaxonomic StatusEmpirical EvidenceMolecular DetailsMolecular TypePresumptive NullSNP Coding ChangeStudentCodon-Taxon-ACodon-PositionCodon-TaxonBCodon-Sitetransition-transversionAminoAcid-Taxon AAA-PositionAminoAcid-Taxon BAberration TypeAberration SizeReference TitleReference AbstractPublication YearMain PMIDRefLinkAdditional PMIDCommentsUser Feedback
2
GP00000958RcMartinRcA7J5U6
Oryza sativa subsp. japonica
CTN5;CYR3;GLC5;TSL7;ASC1;YNL098C;N2198
GO:0046983
GO:0005886;GO:0005634;GO:0005739;GO:0005789
GO:0007165;GO:0032880;GO:0016236;GO:0007190;GO:0030437;GO:0045762;GO:2000222;GO:0000411;GO:0032258;GO:0097271;GO:0010603;GO:0001302
ADR01106MorphologyColoration (seed)
Oryza glaberrima (Africa; wild strains with red pericarp)
Oryza glaberrima (Africa; domesticated strains with white pericarp)
4538Oryza glaberrimaAfrican ricespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
14538Oryza glaberrimaAfrican ricespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
1
Data not curated
DomesticatedCandidate GenePremature stop codon in exon 7CodingYesNonsenseSNP
The molecular basis of white pericarps in African domesticated rice: novel mutations at the Rc gene.
Repeated phenotypic evolution can occur at both the inter- and intraspecific level and is especially prominent in domesticated plants; where artificial selection has favoured the same traits in many different species and varieties. The question of whether repeated evolution reflects changes at the same or different genes in each lineage can now be addressed using the domestication and improvement genes that have been identified in a variety of crops. Here; we document the genetic basis of nonpigmented ('white') pericarps in domesticated African rice (Oryza glaberrima) and compare it with the known genetic basis of the same trait in domesticated Asian rice (Oryza sativa). In some cases; white pericarps in African rice are apparently caused by unique mutations at the Rc gene; which also controls pericarp colour variation in Asian rice. In one case; white pericarps appear to reflect changes at a different gene or potentially a cis-regulatory region.

© 2010 The Authors. Journal Compilation © 2010 European Society For Evolutionary Biology.
201021121088,1ND
3
GP00001026scd-2Martinscd-2O76411
Caenorhabditis elegans
6239.T10H9.2
Belongs to the protein kinase superfamily. Tyr protein kinase family. Insulin receptor subfamily.
T10H9.2GO:0005524;GO:0004714GO:0016021;GO:0005886
GO:0006935;GO:0040024;GO:0007606;GO:0050893
BX284605PhysiologyDiapauseC. elegans - desert strainC. elegans - N26239Caenorhabditis elegansspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
16239
Caenorhabditis elegans
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
1
Data not curated
IntraspecificLinkage MappingGly985Arg, G to ACodingNo
Nonsynonymous
CourtierGGRndAGR1transitionGly985ArgSNP
C. elegans anaplastic lymphoma kinase ortholog SCD-2 controls dauer formation by modulating TGF-beta signaling.
Different environmental stimuli; including exposure to dauer pheromone; food deprivation; and high temperature; can induce C. elegans larvae to enter the dauer stage; a developmentally arrested diapause state. Although molecular and cellular pathways responsible for detecting dauer pheromone and temperature have been defined in part; other sensory inputs are poorly understood; as are the mechanisms by which these diverse sensory inputs are integrated to achieve a consistent developmental outcome.

In this paper; we analyze a wild C. elegans strain isolated from a desert oasis. Unlike wild-type laboratory strains; the desert strain fails to respond to dauer pheromone at 25 degrees C; but it does respond at higher temperatures; suggesting a unique adaptation to the hot desert environment. We map this defect in dauer response to a mutation in the scd-2 gene; which; we show; encodes the nematode anaplastic lymphoma kinase (ALK) homolog; a proto-oncogene receptor tyrosine kinase. scd-2 acts in a genetic pathway shown here to include the HEN-1 ligand; the RTK adaptor SOC-1; and the MAP kinase SMA-5. The SCD-2 pathway modulates TGF-beta signaling; which mediates the response to dauer pheromone; but SCD-2 might mediate a nonpheromone sensory input; such as food.

Our studies identify a new sensory pathway controlling dauer formation and shed light on ALK signaling; integration of signaling pathways; and adaptation to extreme environmental conditions.
200818674914,1
https://sci-hub.tw/10.1016/j.cub.2008.06.060
@GxE
4
GP00001237ETC2ArnoultETC2Q84RD1
Arabidopsis thaliana
3702.AT2G30420.1
ENHANCER OF TRY AND CPC 2;T9D9.23;T9D9_23;At2g30420;T6B20;T9D9
GO:0003700;GO:0043565;GO:0000981;GO:0044212;GO:0001135
GO:0005634
GO:0006355;GO:0006351;GO:0006357;GO:0048629;GO:1900033;GO:0080147
NM_179814.3
MorphologyTrichome density (leaf)Arabidopsis thaliana- Gr-1Arabidopsis thaliana Can-03702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
IntraspecificLinkage MappingK19ECodingNo
Nonsynonymous
CourtierGARndAAR1transitionLys19GluSNP
A single amino acid replacement in ETC2 shapes trichome patterning in natural Arabidopsis populations.
Our understanding of the evolution of organismal diversity is restricted by the current resolution of the genotype-phenotype map. In particular; the genetic basis of environmentally relevant phenotypic variation among natural populations remains poorly understood. Trichomes are single-cell outgrowths on the surface of plant leaves and other above-ground organs. Consistent with trichomes' suggested function to protect plants from predators and abiotic stressors [1-3]; trichome density is strikingly variable among natural populations (e.g.; [2; 4]). Despite substantial progress in the genetic dissection of trichome development [5]; how trichome number is modulated in natural populations remains enigmatic. Here; we show that the ENHANCER OF TRY AND CPC 2 (ETC2) from the single-repeat R3 MYB family is the major locus determining trichome patterning in natural Arabidopsis populations. Our study identifies a single amino acid substitution in ETC2 (K19E) as the causal quantitative trait nucleotide (QTN). We suggest that this amino acid replacement might affect the stability of the ETC2 repressor; which results in a reduced trichome number. This is consistent with the view that morphology can evolve by coding changes that can subtly modulate protein activity as well as cis-regulatory changes that alter expression patterns.
200919818620,1
https://sci-hub.tw/10.1016/j.cub.2009.08.057
functional test of QTN + mutant complementation
5
GP00000195CYC8MartinCYC8P14922
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
4932.YBR112C
Belongs to the CYC8/SSN6 family.
CRT8;SSN6;YBR112C;YBR0908
GO:0042826;GO:0003714;GO:0003713
GO:0005634;GO:0017053
GO:0045944;GO:0006351;GO:0000122;GO:0006338;GO:0035955;GO:0016584;GO:2000531;GO:2001020
X78993Physiology
Salt tolerance (experimental evolution)
Saccharomyces cerevisiaeSaccharomyces cerevisiae4932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
04932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
0
Data not curated
Experimental Evolution
Association Mapping
1bp substitution resulting in premature stop codon
CodingYesNonsenseCourtierTAR464706TAY3transversionTyrndSTPSNP
Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations.
Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong.

Copyright (c) 2010 Elsevier Ltd. All rights reserved.
201020637622,1
https://sci-hub.tw/10.1016/j.cub.2010.06.022
21856932,1
6
GP00000641MDS3MartinMDS3P53094
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
4932.YGL197W
YGL197W;G1307GO:0004977GO:0005737
GO:0051321;GO:0007124;GO:0030435;GO:0075297;GO:0031929
Z72719Physiology
Low-glucose adaptation (experimental evolution)
Saccharomyces cerevisiaeSaccharomyces cerevisiae4932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
04932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
0
Data not curated
Experimental Evolution
Association Mapping
Phe - Val substitutionCodingNo
Nonsynonymous
CourtierTTY126872GTY1transversionPhendValSNP
Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations.
Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong.

Copyright (c) 2010 Elsevier Ltd. All rights reserved.
201020637622,1
https://sci-hub.tw/10.1016/j.cub.2010.06.022
21856932,1
7
GP00000662MKT1MartinMKT1P40850
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
4932.YNL085W
YNL085W;N2302GO:0004520
GO:0034399;GO:0010494;GO:0000932;GO:0005844
GO:0006974;GO:0006281;GO:0044419
X03534Physiology
Low-glucose adaptation (experimental evolution)
Saccharomyces cerevisiae - 30G laboratory strain
Saccharomyces cerevisiae - experimentally evolved lines
4932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
14932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
0
Data not curated
Experimental Evolution
Association Mapping
D30G (reversion; functionally verified); evolved independently in 3 lines
CodingNo
Nonsynonymous
CourtierGAC467221GGC2transitionAsp30GlySNP
Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations.
Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong.

Copyright (c) 2010 Elsevier Ltd. All rights reserved.
201020637622,1
https://sci-hub.tw/10.1016/j.cub.2010.06.022
21856932,1@&
8
GP00000900PMA1MartinPMA1P05030
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
4932.YGL008C
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIIA subfamily.
KTI10;YGL008C
GO:0005524;GO:0046872;GO:0008553
GO:0016021;GO:0005886;GO:0045121
GO:0055085;GO:0006885;GO:1902906;GO:0120029;GO:1902600
X03534Physiology
Salt tolerance (experimental evolution)
Saccharomyces cerevisiae
Saccharomyces cerevisiae - after 500 generations of selective pressure
4932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
04932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
0Taxon A
Experimental Evolution
Association Mapping
Leu363TrpCodingNo
Nonsynonymous
CourtierTTG481584TGG2transversionLeu363TrpSNP
Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations.
Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong.

Copyright (c) 2010 Elsevier Ltd. All rights reserved.
201020637622,1
https://sci-hub.tw/10.1016/j.cub.2010.06.022
21856932.1;25016004.1
PMID 25016004 includes nucleotidic changes
9
GP00000901PMA1MartinPMA1P05030
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
4932.YGL008C
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIIA subfamily.
KTI10;YGL008C
GO:0005524;GO:0046872;GO:0008553
GO:0016021;GO:0005886;GO:0045121
GO:0055085;GO:0006885;GO:1902906;GO:0120029;GO:1902600
X03534Physiology
Salt tolerance (experimental evolution)
Saccharomyces cerevisiae
Saccharomyces cerevisiae - after 500 generations of selective pressure
4932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
04932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
0Taxon A
Experimental Evolution
Association Mapping
Ser234CysCodingNo
Nonsynonymous
CourtierTCY481971TGY2transversionSer234CysSNP
Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations.
Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong.

Copyright (c) 2010 Elsevier Ltd. All rights reserved.
201020637622,1
https://sci-hub.tw/10.1016/j.cub.2010.06.022
21856932.1;25016004.1
PMID 25016004 includes nucleotidic changes
10
GP00001174Vkorc1MartinVKORC1Q9BQB6Homo sapiens
9606.ENSP00000378426
Belongs to the VKOR family.
VKOR;MST134;MST576;VKCFD2;EDTP308;MSTP134;MSTP576;UNQ308/PRO351
GO:0048038;GO:0047057
GO:0016021;GO:0005783;GO:0005789
GO:0017144;GO:0007596;GO:0060348;GO:0017187;GO:0042373
ADN94694Physiology
Xenobiotic resistance (rodenticide; warfarin)
Mus musculus
Mus spretus (North Africa) and Mus musculus (Spain)
10090Mus musculushouse mousespecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
010096Mus spretuswestern wild mousespecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
0
Data not curated
IntraspecificCandidate GeneMultiple coding changesCodingNo
Nonsynonymous
SNP
Adaptive introgression of anticoagulant rodent poison resistance by hybridization between old world mice.
Polymorphisms in the vitamin K 2;3-epoxide reductase subcomponent 1 (vkorc1) of house mice (Mus musculus domesticus) can cause resistance to anticoagulant rodenticides such as warfarin [1-3]. Here we show that resistant house mice can also originate from selection on vkorc1 polymorphisms acquired from the Algerian mouse (M. spretus) through introgressive hybridization. We report on a polymorphic introgressed genomic region in European M. m. domesticus that stems from M. spretus; spans >10 Mb on chromosome 7; and includes the molecular target of anticoagulants vkorc1 [1-4]. We show that in the laboratory; the homozygous complete vkorc1 allele of M. spretus confers resistance when introgressed into M. m. domesticus. Consistent with selection on the introgressed allele after the introduction of rodenticides in the 1950s; we found signatures of selection in patterns of variation in M. m. domesticus. Furthermore; we detected adaptive protein evolution of vkorc1 in M. spretus (Ka/Ks = 1.54-1.93) resulting in radical amino acid substitutions that apparently cause anticoagulant tolerance in M. spretus as a pleiotropic effect. Thus; positive selection produced an adaptive; divergent; and pleiotropic vkorc1 allele in the donor species; M. spretus; which crossed a species barrier and produced an adaptive polymorphic trait in the recipient species; M. m. domesticus.

Copyright © 2011 Elsevier Ltd. All rights reserved.
201121782438,1
https://sci-hub.tw/10.1016/j.cub.2011.06.043
@& @Introgression @Pleiotropy
11
GP00001062SLC45A2=MATPMartinSLC45A2Q9UMX9Homo sapiens
9606.ENSP00000296589
Belongs to the glycoside-pentoside-hexuronide (GPH) cation symporter transporter (TC 2.A.2) family.
1A1;AIM1;MATP;OCA4;SHEP5GO:0008506GO:0016021;GO:0033162
GO:0042438;GO:0048066;GO:0007601;GO:0050896;GO:0015770
XP_005506068
MorphologyColoration (feathers)Columba livia - blue/black
Columba livia - recessive dilute (Dun)
8932Columba liviarock pigeonspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
08932Columba liviarock pigeonspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
0Taxon ADomesticatedLinkage MappingHis341ArgCodingNo
Nonsynonymous
DupuisCAYCGY2transitionHis341ArgSNP
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
Understanding the molecular basis of phenotypic diversity is a critical challenge in biology; yet we know little about the mechanistic effects of different mutations and epistatic relationships among loci that contribute to complex traits. Pigmentation genetics offers a powerful model for identifying mutations underlying diversity and for determining how additional complexity emerges from interactions among loci. Centuries of artificial selection in domestic rock pigeons (Columba livia) have cultivated tremendous variation in plumage pigmentation through the combined effects of dozens of loci. The dominance and epistatic hierarchies of key loci governing this diversity are known through classical genetic studies; but their molecular identities and the mechanisms of their genetic interactions remain unknown. Here we identify protein-coding and cis-regulatory mutations in Tyrp1; Sox10; and Slc45a2 that underlie classical color phenotypes of pigeons and present a mechanistic explanation of their dominance and epistatic relationships. We also find unanticipated allelic heterogeneity at Tyrp1 and Sox10; indicating that color variants evolved repeatedly though mutations in the same genes. These results demonstrate how a spectrum of coding and regulatory mutations in a small number of genes can interact to generate substantial phenotypic diversity in a classic Darwinian model of evolution.

Copyright © 2014 Elsevier Ltd. All rights reserved.
201424508169,1
https://sci-hub.tw/10.1016/j.cub.2014.01.020
@Epistasis
12
GP00001148
tyrosinase-related protein 1 (TYRP1)
MartinTyrp1P07147Mus musculus
10090.ENSMUSP00000006151
Belongs to the tyrosinase family.
b;isa;Oca3;TRP1;Tyrp;TRP-1;brown;Tyrp-1
GO:0042803;GO:0046982;GO:0046872;GO:0004497
GO:0016021;GO:0030669;GO:0010008;GO:0042470;GO:0033162
GO:0032438;GO:0043473;GO:0048023;GO:0006583;GO:0030318;GO:0043438;GO:0006582
NP_001302454
MorphologyColoration (coat)Columba livia - blue/blackColumba livia - ash-red8932Columba liviarock pigeonspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
08932Columba liviarock pigeonspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
0Taxon ADomesticatedLinkage MappingAla23ProCodingNo
Nonsynonymous
WimmerGCNCCN1transitionAla23ProSNP
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
Understanding the molecular basis of phenotypic diversity is a critical challenge in biology; yet we know little about the mechanistic effects of different mutations and epistatic relationships among loci that contribute to complex traits. Pigmentation genetics offers a powerful model for identifying mutations underlying diversity and for determining how additional complexity emerges from interactions among loci. Centuries of artificial selection in domestic rock pigeons (Columba livia) have cultivated tremendous variation in plumage pigmentation through the combined effects of dozens of loci. The dominance and epistatic hierarchies of key loci governing this diversity are known through classical genetic studies; but their molecular identities and the mechanisms of their genetic interactions remain unknown. Here we identify protein-coding and cis-regulatory mutations in Tyrp1; Sox10; and Slc45a2 that underlie classical color phenotypes of pigeons and present a mechanistic explanation of their dominance and epistatic relationships. We also find unanticipated allelic heterogeneity at Tyrp1 and Sox10; indicating that color variants evolved repeatedly though mutations in the same genes. These results demonstrate how a spectrum of coding and regulatory mutations in a small number of genes can interact to generate substantial phenotypic diversity in a classic Darwinian model of evolution.

Copyright © 2014 Elsevier Ltd. All rights reserved.
201424508169,1
https://sci-hub.tw/10.1016/j.cub.2014.01.020
@Epistasis - the ash-red mutation occurred only once and spread species-wide through selective breeding (as the EphB2 mutation for head crest phenotypes)
13
GP00001149
tyrosinase-related protein 1 (TYRP1)
MartinTyrp1P07147Mus musculus
10090.ENSMUSP00000006151
Belongs to the tyrosinase family.
b;isa;Oca3;TRP1;Tyrp;TRP-1;brown;Tyrp-1
GO:0042803;GO:0046982;GO:0046872;GO:0004497
GO:0016021;GO:0030669;GO:0010008;GO:0042470;GO:0033162
GO:0032438;GO:0043473;GO:0048023;GO:0006583;GO:0030318;GO:0043438;GO:0006582
NP_001302454
MorphologyColoration (coat)Columba livia - blue/blackColumba livia - brown b1 allele8932Columba liviarock pigeonspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
08932Columba liviarock pigeonspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
0Taxon ADomesticatedLinkage MappingAla23ProCodingNo
Nonsynonymous
WimmerGCNCCN1transitionAla23ProSNP
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
Understanding the molecular basis of phenotypic diversity is a critical challenge in biology; yet we know little about the mechanistic effects of different mutations and epistatic relationships among loci that contribute to complex traits. Pigmentation genetics offers a powerful model for identifying mutations underlying diversity and for determining how additional complexity emerges from interactions among loci. Centuries of artificial selection in domestic rock pigeons (Columba livia) have cultivated tremendous variation in plumage pigmentation through the combined effects of dozens of loci. The dominance and epistatic hierarchies of key loci governing this diversity are known through classical genetic studies; but their molecular identities and the mechanisms of their genetic interactions remain unknown. Here we identify protein-coding and cis-regulatory mutations in Tyrp1; Sox10; and Slc45a2 that underlie classical color phenotypes of pigeons and present a mechanistic explanation of their dominance and epistatic relationships. We also find unanticipated allelic heterogeneity at Tyrp1 and Sox10; indicating that color variants evolved repeatedly though mutations in the same genes. These results demonstrate how a spectrum of coding and regulatory mutations in a small number of genes can interact to generate substantial phenotypic diversity in a classic Darwinian model of evolution.

Copyright © 2014 Elsevier Ltd. All rights reserved.
201424508169,1
https://sci-hub.tw/10.1016/j.cub.2014.01.020
@Epistasis Multiple alleles
14
GP00001150
tyrosinase-related protein 1 (TYRP1)
MartinTyrp1P07147Mus musculus
10090.ENSMUSP00000006151
Belongs to the tyrosinase family.
b;isa;Oca3;TRP1;Tyrp;TRP-1;brown;Tyrp-1
GO:0042803;GO:0046982;GO:0046872;GO:0004497
GO:0016021;GO:0030669;GO:0010008;GO:0042470;GO:0033162
GO:0032438;GO:0043473;GO:0048023;GO:0006583;GO:0030318;GO:0043438;GO:0006582
NP_001302454
MorphologyColoration (coat)Columba livia - blue/blackColumba livia - brown b2 allele8932Columba liviarock pigeonspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
08932Columba liviarock pigeonspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
0Taxon ADomesticatedLinkage MappingArg72*CodingYesNonsenseWimmerMGATGA1transitionArg72STPSNP
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
Understanding the molecular basis of phenotypic diversity is a critical challenge in biology; yet we know little about the mechanistic effects of different mutations and epistatic relationships among loci that contribute to complex traits. Pigmentation genetics offers a powerful model for identifying mutations underlying diversity and for determining how additional complexity emerges from interactions among loci. Centuries of artificial selection in domestic rock pigeons (Columba livia) have cultivated tremendous variation in plumage pigmentation through the combined effects of dozens of loci. The dominance and epistatic hierarchies of key loci governing this diversity are known through classical genetic studies; but their molecular identities and the mechanisms of their genetic interactions remain unknown. Here we identify protein-coding and cis-regulatory mutations in Tyrp1; Sox10; and Slc45a2 that underlie classical color phenotypes of pigeons and present a mechanistic explanation of their dominance and epistatic relationships. We also find unanticipated allelic heterogeneity at Tyrp1 and Sox10; indicating that color variants evolved repeatedly though mutations in the same genes. These results demonstrate how a spectrum of coding and regulatory mutations in a small number of genes can interact to generate substantial phenotypic diversity in a classic Darwinian model of evolution.

Copyright © 2014 Elsevier Ltd. All rights reserved.
201424508169,1
https://sci-hub.tw/10.1016/j.cub.2014.01.020
@Epistasis Multiple alleles
15
GP00000897plep-1MartinKPt.1GO:0043531GO:0005623GO:0045454CTQ86544Behavior
Male-male copulatory behavior
Caenorhabditis elegans - CB4856 (no plug behavior)
Caenorhabditis elegans - CB4856 (no plug behavior)
6239Caenorhabditis elegansspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
16239
Caenorhabditis elegans
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
1Taxon AIntraspecificLinkage MappingV278DCodingNo
Nonsynonymous
RymGTNGAN2transvertion valine287AspSNP
Natural Variation in plep-1 Causes Male-Male Copulatory Behavior in C. elegans.
In sexual species; gametes have to find and recognize one another. Signaling is thus central to sexual reproduction and involves a rapidly evolving interplay of shared and divergent interests [1-4]. Among Caenorhabditis nematodes; three species have evolved self-fertilization; changing the balance of intersexual relations [5]. Males in these androdioecious species are rare; and the evolutionary interests of hermaphrodites dominate. Signaling has shifted accordingly; with females losing behavioral responses to males [6; 7] and males losing competitive abilities [8; 9]. Males in these species also show variable same-sex and autocopulatory mating behaviors [6; 10]. These behaviors could have evolved by relaxed selection on male function; accumulation of sexually antagonistic alleles that benefit hermaphrodites and harm males [5; 11]; or neither of these; because androdioecy also reduces the ability of populations to respond to selection [12-14]. We have identified the genetic cause of a male-male mating behavior exhibited by geographically dispersed C. elegans isolates; wherein males mate with and deposit copulatory plugs on one another's excretory pores. We find a single locus of major effect that is explained by segregation of a loss-of-function mutation in an uncharacterized gene; plep-1; expressed in the excretory cell in both sexes. Males homozygous for the plep-1 mutation have excretory pores that are attractive or receptive to copulatory behavior of other males. Excretory pore plugs are injurious and hermaphrodite activity is compromised in plep-1 mutants; so the allele might be unconditionally deleterious; persisting in the population because the species' androdioecious mating system limits the reach of selection.

Copyright © 2015 Elsevier Ltd. All rights reserved.
201526455306,1
https://sci-hub.tw/10.1016/j.cub.2015.09.019
@SexualDimorphism
16
GP00001602
Chitin synthase 1 (CHS1)
Prigentchs1H9U0G2Tetranychus urticaechs1;107359084GO:0004100GO:0016021GO:0007166Physiology
Xenobiotic resistance (insecticide; etoxazole acaricide)
spider mite Tetranychus urticae susceptible
spider mite Tetranychus urticae strain HexR and strain005 hexythiazox clofentezine and etoxazole-resistant
32264Tetranychus urticae
two-spotted spider mite
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Trombidiformes; Prostigmata; Eleutherengona; Raphignathae; Tetranychoidea; Tetranychidae; Tetranychus
132264Tetranychus urticae
two-spotted spider mite
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Trombidiformes; Prostigmata; Eleutherengona; Raphignathae; Tetranychoidea; Tetranychidae; Tetranychus
1UnknownIntraspecificLinkage Mapping
A>T p.I1017F (I1056 in D. melanogaster) located in the C-terminal transmembrane domain
CodingNo
Nonsynonymous
WimmerTTATTT3transversionLeu1017PheSNP
High resolution genetic mapping uncovers chitin synthase-1 as the target-site of the structurally diverse mite growth inhibitors clofentezine; hexythiazox and etoxazole in Tetranychus urticae.
The acaricides clofentezine; hexythiazox and etoxazole are commonly referred to as 'mite growth inhibitors'; and clofentezine and hexythiazox have been used successfully for the integrated control of plant mite pests for decades. Although they are still important today; their mode of action has remained elusive. Recently; a mutation in chitin synthase 1 (CHS1) was linked to etoxazole resistance. In this study; we identified and investigated a Tetranychus urticae strain (HexR) harboring recessive; monogenic resistance to each of hexythiazox; clofentezine; and etoxazole. To elucidate if there is a common genetic basis for the observed cross-resistance; we adapted a previously developed bulk segregant analysis method to map with high resolution a single; shared resistance locus for all three compounds. This finding indicates that the underlying molecular basis for resistance to all three compounds is identical. This locus is centered on the CHS1 gene; and as supported by additional genetic and biochemical studies; a non-synonymous variant (I1017F) in CHS1 associates with resistance to each of the tested acaricides in HexR. Our findings thus demonstrate a shared molecular mode of action for the chemically diverse mite growth inhibitors clofentezine; hexythiazox and etoxazole as inhibitors of an essential; non-catalytic activity of CHS1. Given the previously documented cross-resistance between clofentezine; hexythiazox and the benzyolphenylurea (BPU) compounds flufenoxuron and cycloxuron; CHS1 should be also considered as a potential target-site of insecticidal BPUs.

Copyright © 2014 Elsevier Ltd. All rights reserved.
201424859419,1
https://sci-hub.tw/10.1016/j.ibmb.2014.05.004
22393009,1
Observed pattern is indicative of recurrent mutation and selection in EtoxR and Strain005. Transgenic flies with the same mutation is highly resistant to etoxazole and all tested benzoylureas as well as buprofezin
17
GP00000841para (kdr)MartinparaP35500
Drosophila melanogaster
7227.FBpp0303597
Belongs to the sodium channel (TC 1.A.1.10) family. Para subfamily.
bas;bss;CG9907;Dmel\CG9907;DmNav;DmNav1;DmNa[[v]];DmNa[[V]];DmNa[[v]]1;l(1)14Da;l(1)ESHS48;lincRNA.S9469;Nav1;Ocd;olfD;par;sbl;sbl-1;Shu;Shudderer
GO:0005509;GO:0005244;GO:0005248;GO:0005272
GO:0005887;GO:0001518
GO:0019228;GO:0045433;GO:0001666;GO:0009612;GO:0034765;GO:0086010;GO:0035725;GO:0007638;GO:0060078
Physiology
Xenobiotic resistance (insecticide)
Leptinotarsa decemlineata
Leptinotarsa decemlineata - resistant
7539
Leptinotarsa decemlineata
Colorado potato beetle
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Coleoptera; Polyphaga; Cucujiformia; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Doryphorini; Leptinotarsa
07539
Leptinotarsa decemlineata
Colorado potato beetle
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Coleoptera; Polyphaga; Cucujiformia; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Doryphorini; Leptinotarsa
0Taxon AIntraspecificCandidate GeneL1014HCodingNo
Nonsynonymous
WimmerCTYCAY2transversionLeu1014HisSNP
Diversity and Convergence of Sodium Channel Mutations Involved in Resistance to Pyrethroids.
Pyrethroid insecticides target voltage-gated sodium channels; which are critical for electrical signaling in the nervous system. The intensive use of pyrethroids in controlling arthropod pests and disease vectors has led to many instances of pyrethroid resistance around the globe. In the past two decades; studies have identified a large number of sodium channel mutations that are associated with resistance to pyrethroids. The purpose of this review is to summarize both common and unique sodium channel mutations that have been identified in arthropod pests of importance to agriculture or human health. Identification of these mutations provides valuable molecular markers for resistance monitoring in the field and helped the discovery of the elusive pyrethroid receptor site(s) on the sodium channel.
201324019556,1
https://sci-hub.tw/10.1016/j.pestbp.2013.02.007
18
GP00001118
teosinte glume architecture (tga1)
MartinTGA1Q39237
Arabidopsis thaliana
3702.AT5G65210.1
Belongs to the bZIP family.
MQN23.15;MQN23_15;TGACG sequence-specific binding protein 1;BZIP47;At5g65210
GO:0003700;GO:0043565;GO:0044212
GO:0005634GO:0006351;GO:0042742AEP96351MorphologyCupule retraction
Zea mays ssp. parviglumis and mexicana (teosinthe)
Zea mays ssp. mays4577Zea maysspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea
14577Zea maysspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea
1
Data not curated
DomesticatedLinkage Mapping
K6N; the lysine residue being conserved in rice and wheat
CodingNo
Nonsynonymous
WimmerAARAAY3transversionLys6AsnSNP
The origin of the naked grains of maize.
The most critical step in maize (Zea mays ssp. mays) domestication was the liberation of the kernel from the hardened; protective casing that envelops the kernel in the maize progenitor; teosinte. This evolutionary step exposed the kernel on the surface of the ear; such that it could readily be used by humans as a food source. Here we show that this key event in maize domestication is controlled by a single gene (teosinte glume architecture or tga1); belonging to the SBP-domain family of transcriptional regulators. The factor controlling the phenotypic difference between maize and teosinte maps to a 1-kilobase region; within which maize and teosinte show only seven fixed differences in their DNA sequences. One of these differences encodes a non-conservative amino acid substitution and may affect protein function; and the other six differences potentially affect gene regulation. Molecular evolution analyses show that this region was the target of selection during maize domestication. Our results demonstrate that modest genetic changes in single genes can induce dramatic changes in phenotype during domestication and evolution.
200516079849,1
https://sci-hub.tw/10.1038/nature03863
19
GP00001047SHELLMartinAGL11Q38836
Arabidopsis thaliana
3702.AT4G09960.3
AGAMOUS-like 11;AGL11;SEEDSTICK;T5L19.90;T5L19_90;STK;At4g09960
GO:0046983;GO:0003700;GO:0000977
GO:0005634
GO:0007275;GO:0045944;GO:0006351
MorphologyFruit shell thicknessElaeis guineensis; thick shelled
Elaeis guineensis; thin shelled (Nigeria)
51953Elaeis guineensisAfrican oil palmspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Arecales; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis
051953Elaeis guineensisAfrican oil palmspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Arecales; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis
1
Data not curated
DomesticatedLinkage Mapping
1a.a substitution in DNA binding domain
CodingNo
Nonsynonymous
WimmerAARAAY3transversionLys128AsnSNP
The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK.
A key event in the domestication and breeding of the oil palm Elaeis guineensis was loss of the thick coconut-like shell surrounding the kernel. Modern E. guineensis has three fruit forms; dura (thick-shelled); pisifera (shell-less) and tenera (thin-shelled); a hybrid between dura and pisifera. The pisifera palm is usually female-sterile. The tenera palm yields far more oil than dura; and is the basis for commercial palm oil production in all of southeast Asia. Here we describe the mapping and identification of the SHELL gene responsible for the different fruit forms. Using homozygosity mapping by sequencing; we found two independent mutations in the DNA-binding domain of a homologue of the MADS-box gene SEEDSTICK (STK; also known as AGAMOUS-LIKE 11); which controls ovule identity and seed development in Arabidopsis. The SHELL gene is responsible for the tenera phenotype in both cultivated and wild palms from sub-Saharan Africa; and our findings provide a genetic explanation for the single gene hybrid vigour (or heterosis) attributed to SHELL; via heterodimerization. This gene mutation explains the single most important economic trait in oil palm; and has implications for the competing interests of global edible oil production; biofuels and rainforest conservation.
201323883930,1
https://sci-hub.tw/10.1038/nature12356
20
GP00001048SHELLMartinAGL11Q38836
Arabidopsis thaliana
3702.AT4G09960.3
AGAMOUS-like 11;AGL11;SEEDSTICK;T5L19.90;T5L19_90;STK;At4g09960
GO:0046983;GO:0003700;GO:0000977
GO:0005634
GO:0007275;GO:0045944;GO:0006351
MorphologyFruit shell thicknessElaeis guineensis; thick shelled
Elaeis guineensis; thin shelled (Congo)
51953Elaeis guineensisAfrican oil palmspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Arecales; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis
051953Elaeis guineensisAfrican oil palmspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Arecales; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis
1
Data not curated
DomesticatedCandidate Gene
1a.a substitution in DNA binding domain
CodingNo
Nonsynonymous
WimmerCTNCCN2transitionLeu128ProSNP
The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK.
A key event in the domestication and breeding of the oil palm Elaeis guineensis was loss of the thick coconut-like shell surrounding the kernel. Modern E. guineensis has three fruit forms; dura (thick-shelled); pisifera (shell-less) and tenera (thin-shelled); a hybrid between dura and pisifera. The pisifera palm is usually female-sterile. The tenera palm yields far more oil than dura; and is the basis for commercial palm oil production in all of southeast Asia. Here we describe the mapping and identification of the SHELL gene responsible for the different fruit forms. Using homozygosity mapping by sequencing; we found two independent mutations in the DNA-binding domain of a homologue of the MADS-box gene SEEDSTICK (STK; also known as AGAMOUS-LIKE 11); which controls ovule identity and seed development in Arabidopsis. The SHELL gene is responsible for the tenera phenotype in both cultivated and wild palms from sub-Saharan Africa; and our findings provide a genetic explanation for the single gene hybrid vigour (or heterosis) attributed to SHELL; via heterodimerization. This gene mutation explains the single most important economic trait in oil palm; and has implications for the competing interests of global edible oil production; biofuels and rainforest conservation.
201323883930,1
https://sci-hub.tw/10.1038/nature12356
21
GP00000099APOE (apolipoprotein E)MartinAPOEP02649Homo sapiens
9606.ENSP00000252486
Belongs to the apolipoprotein A1/A4/E family.
AD2;LPG;APO-E;ApoE4;LDLCQ5
GO:0042802;GO:0046983;GO:0042803;GO:0001540;GO:0016209;GO:0015485;GO:0017127;GO:0008201;GO:0008289;GO:0005319;GO:0071813;GO:0050750;GO:0046911;GO:0060228;GO:0005543;GO:0044877;GO:0005198;GO:0048156;GO:0070326
GO:0005886;GO:0005737;GO:0016020;GO:0070062;GO:0005634;GO:0005576;GO:0005794;GO:0043083;GO:0031012;GO:0062023;GO:0005615;GO:0072562;GO:0042627;GO:0030669;GO:0030425;GO:0034365;GO:0005769;GO:0071682;GO:0005783;GO:0005788;GO:1903561;GO:0034364;GO:0034363;GO:1990777;GO:0034362;GO:0043025;GO:0034361;GO:0098978
GO:0033344;GO:0097113;GO:0042982;GO:0048844;GO:0006874;GO:0044267;GO:0019934;GO:0006707;GO:0042632;GO:0008203;GO:0034378;GO:0034382;GO:0034371;GO:0007010;GO:0055089;GO:0007186;GO:0034380;GO:0034384;GO:0034375;GO:0046907;GO:0010877;GO:0042158;GO:0042159;GO:0035641;GO:0015909;GO:0007616;GO:0034374;GO:0051651;GO:1902430;GO:0030195;GO:0043537;GO:0090090;GO:0032269;GO:0045541;GO:0090370;GO:0061000;GO:1902951;GO:0001937;GO:0010629;GO:0050728;GO:0051055;GO:1903001;GO:1900272;GO:0043407;GO:0043524;GO:1901215;GO:0010977;GO:1902999;GO:0010544;GO:1901627;GO:1901630;GO:0090209;GO:0031102;GO:0007263;GO:0097114;GO:0033700;GO:0044794;GO:1905908;GO:1902004;GO:0010875;GO:0010873;GO:0060999;GO:1902952;GO:0045807;GO:1905855;GO:1905860;GO:0046889;GO:1903002;GO:0032805;GO:0051044;GO:1902998;GO:1901216;GO:0010976;GO:0051000;GO:1902995;GO:1901628;GO:1901631;GO:0043687;GO:0017038;GO:0006898;GO:1905906;GO:1900221;GO:0030516;GO:2000822;GO:0032489;GO:1905890;GO:0090181;GO:1901214;GO:0048168;GO:0032462;GO:0051246;GO:1902947;GO:0006357;GO:0061771;GO:0002021;GO:0000302;GO:0001523;GO:0043691;GO:0007271;GO:0019433;GO:0070328;GO:0006641;GO:0042311;GO:0034447;GO:0034372;GO:0019068
NP_001289617
PhysiologyAgingHomo sapiensHomo sapiens9606Homo sapienshumanspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
09606Homo sapienshumanspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
0
Data not curated
Intraspecific
Association Mapping
Cys112ArgCodingNo
Nonsynonymous
DupuisTGYCGYtransitionCys112ArgSNP
Variants near CHRNA3/5 and APOE have age- and sex-related effects on human lifespan.
Lifespan is a trait of enormous personal interest. Research into the biological basis of human lifespan; however; is hampered by the long time to death. Using a novel approach of regressing (272;081) parental lifespans beyond age 40 years on participant genotype in a new large data set (UK Biobank); we here show that common variants near the apolipoprotein E and nicotinic acetylcholine receptor subunit alpha 5 genes are associated with lifespan. The effects are strongly sex and age dependent; with APOE ɛ4 differentially influencing maternal lifespan (P=4.2 × 10(-15); effect -1.24 years of maternal life per imputed risk allele in parent; sex difference; P=0.011); and a locus near CHRNA3/5 differentially affecting paternal lifespan (P=4.8 × 10(-11); effect -0.86 years per allele; sex difference P=0.075). Rare homozygous carriers of the risk alleles at both loci are predicted to have 3.3-3.7 years shorter lives.
201627029810,1
https://sci-hub.tw/10.1038/ncomms11174
LD with SNP previously associated to other age-related conditions and traits including Alzheimer
22
GP00001346tyrosinase (TYR)PrigentTyrP11344Mus musculus
10090.ENSMUSP00000004770
Belongs to the tyrosinase family.
c;Oca1;skc35;albino
GO:0042803;GO:0046982;GO:0005507;GO:0004503
GO:0016021;GO:0005737;GO:0005829;GO:0005634;GO:0043231;GO:0048471;GO:0042470;GO:0033162
GO:0042438;GO:0043473;GO:0008283;GO:0033280;GO:0051591;GO:0009411;GO:0048538
MorphologyColoration (skin)Lion-Wild typeLion-white coat9689Panthera leolionspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae; Panthera
09689Panthera leolionspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae; Panthera
0Taxon AIntraspecific
Association Mapping
c.260G>A p.Arg87GlnCodingNo
Nonsynonymous
WimmerCGNCAR2transitionArg87GlnSNP
The tiger genome and comparative analysis with lion and snow leopard genomes.
Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger; African lion; white African lion and snow leopard. Through comparative genetic analyses of these genomes; we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39); which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close; but distinct; species.
201324045858,1
https://sci-hub.tw/10.1038/ncomms3433
23
GP00001357EPAS1PrigentEPAS1Q99814Homo sapiens
9606.ENSP00000263734
HLF;MOP2;ECYT4;HIF2A;PASD2;bHLHe73;BHLHE73
GO:0046982;GO:0043565;GO:0008134;GO:0003677;GO:0000981;GO:0001077;GO:0035035
GO:0005829;GO:0005654;GO:0005634;GO:0005667;GO:0016607
GO:0045944;GO:0043687;GO:0007165;GO:0030324;GO:0071456;GO:0061418;GO:0001666;GO:0001525;GO:0001974;GO:0048469;GO:0001892;GO:0030218;GO:0055072;GO:0007005;GO:0048625;GO:0042415;GO:0120162;GO:0002027;GO:0043619;GO:0043129;GO:0006366;GO:0007601
PhysiologyHypoxia response
Panthera spp + Neofilis clouded leopard
snow leopard9688Pantheragenus
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae
029064Panthera unciasnow leopardspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae; Panthera
0Taxon AInterspecific
Association Mapping
Ile663 and Arg794CodingNo
Nonsynonymous
SNP
The tiger genome and comparative analysis with lion and snow leopard genomes.
Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger; African lion; white African lion and snow leopard. Through comparative genetic analyses of these genomes; we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39); which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close; but distinct; species.
201324045858,1
https://sci-hub.tw/10.1038/ncomms3433
putative candidate
24
GP00001358EGLN1PrigentEGLN1Q9GZT9Homo sapiens
9606.ENSP00000355601
HPH2;PHD2;SM20;ECYT3;HALAH;HPH-2;HIFPH2;ZMYND6;C1orf12;HIF-PH2;PNAS-118;PNAS-137
GO:0016706;GO:0019899;GO:0008198;GO:0031418;GO:0031545;GO:0031543
GO:0005737;GO:0005829;GO:0005634;GO:0014069;GO:0098978
GO:0045944;GO:1901214;GO:0006879;GO:0055008;GO:0060347;GO:0060711;GO:0051344;GO:0043433;GO:0032364;GO:0018401;GO:0045765;GO:0061418;GO:0001666;GO:0071731;GO:0060412;GO:0099175;GO:0099576
PhysiologyHypoxia response
Panthera spp + Neofilis clouded leopard
snow leopard9688Pantheragenus
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae
029064Panthera unciasnow leopardspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae; Panthera
0Taxon AInterspecific
Association Mapping
p.Met39LysCodingNo
Nonsynonymous
DupuisATGAAGtransversionMetLysSNP
The tiger genome and comparative analysis with lion and snow leopard genomes.
Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger; African lion; white African lion and snow leopard. Through comparative genetic analyses of these genomes; we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39); which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close; but distinct; species.
201324045858,1
https://sci-hub.tw/10.1038/ncomms3433
putative candidate
25
GP00001421AquaporinPrigentAQP1P29972Homo sapiens
9606.ENSP00000311165
Belongs to the MIP/aquaporin (TC 1.A.8) family.
CO;CHIP28;AQP-CHIP
GO:0042802;GO:0015079;GO:0015250;GO:0008519;GO:0022857;GO:0035379;GO:0015168;GO:0005223;GO:0030184;GO:0005267;GO:0005372
GO:0005886;GO:0016324;GO:0005737;GO:0070062;GO:0005887;GO:0005634;GO:0016323;GO:0031965;GO:0045177;GO:0005903;GO:0042383;GO:0031526;GO:0009925;GO:0020003
GO:0043066;GO:0019934;GO:0006813;GO:0071260;GO:0042493;GO:0071280;GO:0003091;GO:0071456;GO:0006833;GO:0071300;GO:0042476;GO:0070301;GO:0071732;GO:0015701;GO:0030185;GO:0045766;GO:0043154;GO:0048146;GO:0071320;GO:0015696;GO:0071549;GO:0034644;GO:0030157;GO:0035378;GO:0015670;GO:0006884;GO:0019725;GO:0071474;GO:0071241;GO:0071288;GO:0071472;GO:0033326;GO:0030950;GO:0015793;GO:0021670;GO:0085018;GO:0050891;GO:0046878;GO:0003097;GO:0035377
AB281620Physiology
Water transport (selective accumulation of water or glycerol)
BgAqp Aquaporin water selective channel
PvAqp2 aquaglyceroporin glycerol transporter
6973Blattella germanicaGerman cockroachspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Polyneoptera; Dictyoptera; Blattodea; Blaberoidea; Ectobiidae; Blattellinae; Blattella
0319348
Polypedilum vanderplanki
sleeping chironomidspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Polypedilum; Polypedilum
0UnknownInterspecificCandidate Genep.His174AlaCodingNo
Nonsynonymous
DupuisCAYGCN???HisAlaSNP
Insect glycerol transporters evolved by functional co-option and gene replacement.
Transmembrane glycerol transport is typically facilitated by aquaglyceroporins in Prokaryota and Eukaryota. In holometabolan insects however; aquaglyceroporins are absent; yet several species possess polyol permeable aquaporins. It thus remains unknown how glycerol transport evolved in the Holometabola. By combining phylogenetic and functional studies; here we show that a more efficient form of glycerol transporter related to the water-selective channel AQP4 specifically evolved and multiplied in the insect lineage; resulting in the replacement of the ancestral branch of aquaglyceroporins in holometabolan insects. To recapitulate this evolutionary process; we generate specific mutants in distantly related insect aquaporins and human AQP4 and show that a single mutation in the selectivity filter converted a water-selective channel into a glycerol transporter at the root of the crown clade of hexapod insects. Integration of phanerozoic climate models suggests that these events were associated with the emergence of complete metamorphosis and the unparalleled radiation of insects.
201526183829,1
https://sci-hub.tw/10.1038/ncomms8814
ancestry is difficult to understand because phylogenetic tree seems to show the opposite of the article's conclusion
26
GP00001023SBNO1MartinSBNO1A3KN83Homo sapiens
9606.ENSP00000387361
Belongs to the SBNO family.Sno;MOP3
GO:0046872;GO:0009055;GO:0051537;GO:0015035
GO:0005737;GO:0005634GO:0006355BC133704MorphologyHead size
Homo sapiens - European ancestry
Homo sapiens - European ancestry
9606Homo sapienshumanspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
09606Homo sapienshumanspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
0
Data not curated
Intraspecific
Association Mapping
Ser729AsnCodingNo
Nonsynonymous
PintonAGYAAY2transitionSer729AsnSNP
Common variants at 12q15 and 12q24 are associated with infant head circumference.
To identify genetic variants associated with head circumference in infancy; we performed a meta-analysis of seven genome-wide association studies (GWAS) (N = 10;768 individuals of European ancestry enrolled in pregnancy and/or birth cohorts) and followed up three lead signals in six replication studies (combined N = 19;089). rs7980687 on chromosome 12q24 (P = 8.1 × 10(-9)) and rs1042725 on chromosome 12q15 (P = 2.8 × 10(-10)) were robustly associated with head circumference in infancy. Although these loci have previously been associated with adult height; their effects on infant head circumference were largely independent of height (P = 3.8 × 10(-7) for rs7980687 and P = 1.3 × 10(-7) for rs1042725 after adjustment for infant height). A third signal; rs11655470 on chromosome 17q21; showed suggestive evidence of association with head circumference (P = 3.9 × 10(-6)). SNPs correlated to the 17q21 signal have shown genome-wide association with adult intracranial volume; Parkinson's disease and other neurodegenerative diseases; indicating that a common genetic variant in this region might link early brain growth with neurological disease in later life.
201222504419,1
https://sci-hub.tw/10.1038/ng.2238
27
GP00001042Shattering1 - Sh1MartinYAB2Q10FZ7
Oryza sativa subsp. japonica
39947.LOC_Os03g44710.1
Belongs to the YABBY family.
FIL2;YAB2;YABBY;OsYAB2;OsYABBY2;Os03g0650000;LOC_Os03g44710
GO:0046872GO:0005634GO:0007275PhysiologySeed shattering
Sorghum virgatum - shattering
Sorghum bicolor; SC265-like non-shattering
1428165Sorghum virgatumspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
04113Solanum tuberosumpotatospecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
1
Data not curated
DomesticatedLinkage MappingGT-to-GG splice-site variantCodingNoSNP
Parallel domestication of the Shattering1 genes in cereals.
A key step during crop domestication is the loss of seed shattering. Here; we show that seed shattering in sorghum is controlled by a single gene; Shattering1 (Sh1); which encodes a YABBY transcription factor. Domesticated sorghums harbor three different mutations at the Sh1 locus. Variants at regulatory sites in the promoter and intronic regions lead to a low level of expression; a 2.2-kb deletion causes a truncated transcript that lacks exons 2 and 3; and a GT-to-GG splice-site variant in the intron 4 results in removal of the exon 4. The distributions of these non-shattering haplotypes among sorghum landraces suggest three independent origins. The function of the rice ortholog (OsSh1) was subsequently validated with a shattering-resistant mutant; and two maize orthologs (ZmSh1-1 and ZmSh1-5.1+ZmSh1-5.2) were verified with a large mapping population. Our results indicate that Sh1 genes for seed shattering were under parallel selection during sorghum; rice and maize domestication.
201222581231,1
https://sci-hub.tw/10.1038/ng.2281
@Splicing Verify Orthology
28
GP00000679MTH1MartinCUP1-1P0CX80
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
4932.YHR055C
Belongs to the metallothionein superfamily. Type 12 family.
CUP1;MTH1;YHR053C
GO:0016209;GO:0005507;GO:0046870;GO:0004784
GO:0005829
GO:0071585;GO:0010273;GO:0046688;GO:0019430
K02204Physiology
Low-glucose adaptation (experimental evolution)
Saccharomyces cerevisiaeSaccharomyces cerevisiae4932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
04932
Saccharomyces cerevisiae
baker's yeastspecies
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
0
Data not curated
Experimental Evolution
Association Mapping
1bp substitution resulting in premature stop codon
CodingYesNonsenseWimmerTCRTAR2transversionSer441STPSNP
Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae.
The classical model of adaptive evolution in an asexual population postulates that each adaptive clone is derived from the one preceding it. However; experimental evidence has suggested more complex dynamics; with theory predicting the fixation probability of a beneficial mutation as dependent on the mutation rate; population size and the mutation's selection coefficient. Clonal interference has been demonstrated in viruses and bacteria but not in a eukaryote; and a detailed molecular characterization is lacking. Here we use three different fluorescent markers to visualize the dynamics of asexually evolving yeast populations. For each adaptive clone within one of our evolving populations; we identified the underlying mutations; monitored their population frequencies and used microarrays to characterize changes in the transcriptome. These results represent the most detailed molecular characterization of experimental evolution to date and provide direct experimental evidence supporting both the clonal interference and the multiple mutation models.
200819029899,1https://sci-hub.tw/10.1038/ng.28021552329,1
29
GP00001510kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 7.70 hours from Vietnam (5 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
D353Y affecting the BTB/POZ domainCodingNo
Nonsynonymous
PintonGAYTAY1transversionAsp353TyrSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
30
GP00001511kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.34 hours from Myanmar (5 samples) and Thailand (6 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
P441L affecting the BTB/POZ domainCodingNo
Nonsynonymous
Barthome
CCNCTN2transitionPro441LeuSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
31
GP00001512kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.02 hours from Myanmar (3 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
F446I affecting the encoded propeller and BTB/POZ domains
CodingNo
Nonsynonymous
Barthome
TTYATY1transversionPhe446IleSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
32
GP00001513kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.55 hours from Myanmar (2 samples) Thailand (3 samples) and Cambodia (2 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
G449A affecting the encoded propeller and BTB/POZ domains
CodingNo
Nonsynonymous
Barthome
GGNGCN3transversionGly449AlaSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
33
GP00001514kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 8.38 hours from Thailand (6 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
N458Y affecting the encoded propeller and BTB/POZ domains
CodingNo
Nonsynonymous
Barthome
AAYTAY1transversionAsn458TyrSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
34
GP00001515kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.13 hours from Thailand (1 sample) and Cambodia (2 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
A481V affecting the encoded propeller domain
CodingNo
Nonsynonymous
Barthome
GCNGTN2transitionAla481ValSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
35
GP00001516kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.76 hours from Cambodia (45 samples) and Vietnam (4 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Tyr493His affecting the encoded propeller domain
CodingNo
Nonsynonymous
Barthome
TAYCAY1transitionTyr493HisSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
36
GP00001517kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 4.68 hours from Thailand (1 sample)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
N525D affecting the encoded propeller domain
CodingNo
Nonsynonymous
Barthome
AAYGAY1transitionAsn525AspSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
37
GP00001518kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.02 hours from Thailand (1 sample)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
N537I affecting the encoded propeller domain
CodingNo
Nonsynonymous
Barthome
AAYATH2transversionAsn537IleSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
38
GP00001519kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.70 hours from Thailand (13 samples) Laos (2 samples) Cambodia (25 samples) and Vietnam (4 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Arg539Thr affecting the encoded propeller domain
CodingNo
Nonsynonymous
Barthome
AGNACN2transversionArg539ThrSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
39
GP00001520kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 7.07 hours from Cambodia (2 samples) and Vietnam (22 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Ile543Thr affecting the encoded propeller domain
CodingNo
Nonsynonymous
Barthome
ATHACH2transitionIle543ThrSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
40
GP00001521kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.03 hours from Thailand (2 samples) and Vietnam (9 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Pro553Leu affecting the encoded propeller domain
CodingNo
Nonsynonymous
CortierCCYndCTY2transitionPro553LeuSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
41
GP00001522kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.93 hours from Myanmar (2 samples) and Thailande (5 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
R561H affecting the encoded propeller domain
CodingNo
Nonsynonymous
CortierCGYndCAY2transitionArg561HistSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
42
GP00001523kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.67 hours from Vietnam (5 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
V568G affecting the encoded propeller domain
CodingNo
Nonsynonymous
CortierGTYndGGY2transversionVal568GlySNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
43
GP00001524kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.85 hours from Myanmar (6 samples) and Thailand (1 sample)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
P574L affecting the encoded propeller domain
CodingNo
Nonsynonymous
CortierCTYndCCY2tranitionPro574LeuSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
44
GP00001525kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.72 hours from Myanmar (11 samples) Thailand (21 samples) Cambodia (241 samples) and Vietnam (9 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Cys580Tyr affecting the encoded propeller domain
CodingNo
Nonsynonymous
CortierTGYndTAY2transversionCys580TyrSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
k13-C580Y the most widespread resistance allele has originated independently in multiple locations
45
GP00001526kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.41 hours from Cambodia (2 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
D584V affecting the encoded propeller domain
CodingNo
Nonsynonymous
CortierGAYndGTY2tranversionAsp584ValSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
46
GP00001527kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.32 hours from Myanmar (2 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
F673I affecting the encoded propeller domain
CodingNo
Nonsynonymous
CortierTTYndATY1transversionPhe678IleSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
47
GP00001528kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.60 hours from Myanmar (2 samples) and Thailand (11 samples)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
A675V affecting the encoded propeller domain
CodingNo
Nonsynonymous
CortierGCYndGTY2transitionAla675ValSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
48
GP00001529kelch 13Prigent
PF3D7_1343700
Q8IDQ2
Plasmodium falciparum (isolate 3D7)
PF3D7_1343700GO:0003677;GO:0003682GO:0031463
GO:0016567;GO:0042493;GO:0051260
KM187892.1
Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.80 hours from Cambodia (1 sample)
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
H719N affecting the encoded propeller domain
CodingNo
Nonsynonymous
CortierCAYndAAY1transversionHis719AsnSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
49
GP00001530ferredoxinPrigent
PF3D7_1318100
Q8IED5
Plasmodium falciparum (isolate 3D7)
Belongs to the 2Fe2S plant-type ferredoxin family.
PF3D7_1318100
GO:0046872;GO:0009055;GO:0051537
GO:0020011GO:0055114Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.53 h
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Asp193TyrCodingNo
Nonsynonymous
MousGAYTAY1transversionAsp193TyrSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
50
GP00001531
apicoplast ribosomal protein S10
Prigent
PF3D7_1460900.1
Q8IKM3
Plasmodium falciparum (isolate 3D7)
PF3D7_1460900.1GO:0003735GO:0005739;GO:0015935GO:0006412Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.58 h
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Val127MetCodingNo
Nonsynonymous
MousGTGATG1transitionVal127MetSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
51
GP00001532
multidrug resistance protein 2
Prigent
PF3D7_1447900
Q8IKZ6
Plasmodium falciparum (isolate 3D7)
PF3D7_1447900
GO:0005524;GO:0042626;GO:0008559;GO:0046872;GO:0046873
GO:0016021;GO:0005773GO:0006855Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.54 h
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Thr484IleCodingNo
Nonsynonymous
MousACHATH2transitionThr484IleSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
52
GP00001533
chloroquine resistance transporter
PrigentCRTQ9N623
Plasmodium falciparum
Belongs to the CRT-like transporter family.
PF3D7_1447900GO:0015238GO:0016021;GO:0005774GO:0006855Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.47 h
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Ile356ThrCodingNo
Nonsynonymous
MousATHACH2transitionIle356ThrSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
53
GP00001534protein phosphatasePrigent
PF3D7_1012700
Q8IJR8
Plasmodium falciparum (isolate 3D7)
PF3D7_1012700GO:0008420GO:0016591GO:0070940Physiology
Xenobiotic resistance (artemisinin)
Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours
Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.52 h
5833Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
05833
Plasmodium falciparum
malaria parasite P. falciparum
species
cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania)
0Taxon AIntraspecific
Association Mapping
p.Val1157LeuCodingNo
Nonsynonymous
MousGTN490720
YTR, CTN
1transversionVal1157LeuSNP
Genetic architecture of artemisinin-resistant Plasmodium falciparum.
We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.
201525599401,1
https://sci-hub.tw/10.1038/ng.3189
54
GP00001444CREBRFPrigentCREBRFQ8IUR6Homo sapiens
9606.ENSP00000296953
Belongs to the bZIP family. CREBRF subfamily.
LRF;C5orf41
GO:0000977;GO:0001228;GO:0000981
GO:0005737;GO:0005654;GO:0005634;GO:0016604
GO:0045944;GO:0000122;GO:0042711;GO:0030968;GO:0034976;GO:0045732;GO:1900102;GO:1900170;GO:0032388;GO:1902213;GO:0051222
NM_153607
MorphologyBody size (obesity)
human Samoan not associated with higher BMI
human Samoan associated with higher BMI
9606Homo sapienshumanspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
09606Homo sapienshumanspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
0Taxon AIntraspecific
Association Mapping
c.1370G>A p.Arg457GlnCodingNo
Nonsynonymous
MousSNP
A thrifty variant in CREBRF strongly influences body mass index in Samoans.
Samoans are a unique founder population with a high prevalence of obesity; making them well suited for identifying new genetic contributors to obesity. We conducted a genome-wide association study (GWAS) in 3;072 Samoans; discovered a variant; rs12513649; strongly associated with body mass index (BMI) (P = 5.3 × 10(-14)); and replicated the association in 2;102 additional Samoans (P = 1.2 × 10(-9)). Targeted sequencing identified a strongly associated missense variant; rs373863828 (p.Arg457Gln); in CREBRF (meta P = 1.4 × 10(-20)). Although this variant is extremely rare in other populations; it is common in Samoans (frequency of 0.259); with an effect size much larger than that of any other known common BMI risk variant (1.36-1.45 kg/m(2) per copy of the risk-associated allele). In comparison to wild-type CREBRF; the Arg457Gln variant when overexpressed selectively decreased energy use and increased fat storage in an adipocyte cell model. These data; in combination with evidence of positive selection of the allele encoding p.Arg457Gln; support a 'thrifty' variant hypothesis as a factor in human obesity.
201627455349,1
https://sci-hub.tw/10.1038/ng.3620
55
GP00000873phytochrome C (PHYC)MartinPHYCP14714
Arabidopsis thaliana
3702.AT5G35840.1
Belongs to the phytochrome family.
MIK22.15;MIK22_15;phytochrome C;PHYTOCHROME C;At5g35840
GO:0042803;GO:0009881
GO:0005829;GO:0005634;GO:0016604;GO:0016607
GO:0006355;GO:0006351;GO:0018298;GO:0009585;GO:0009584;GO:0017006
X17343PhysiologyLight sensitivityArabidopsis thaliana- Col0Arabidopsis thaliana- Fr-23702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
IntraspecificLinkage Mapping
K299*; the predicted Fr-2 PHYC protein therefore lacks half of the GAF domain; and the entire PHY; PAS and histidine kinase domains; all of which are typically required for phytochrome function
CodingYesNonsenseMousSNP
The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana.
Light has an important role in modulating seedling growth and flowering time. We show that allelic variation at the PHYTOCHROME C (PHYC) photoreceptor locus affects both traits in natural populations of A. thaliana. Two functionally distinct PHYC haplotype groups are distributed in a latitudinal cline dependent on FRIGIDA; a locus that together with FLOWERING LOCUS C explains a large portion of the variation in A. thaliana flowering time. In a genome-wide scan for association of 65 loci with latitude; there was an excess of significant P values; indicative of population structure. Nevertheless; PHYC was the most strongly associated locus across 163 strains; suggesting that PHYC alleles are under diversifying selection in A. thaliana. Our work; together with previous findings; suggests that photoreceptor genes are major agents of natural variation in plant flowering and growth response.
200616732287,1
https://sci-hub.tw/10.1038/ng1818
56
GP00000786
opsin - rhodopsin1 (RH1)
MartinRHOP08100Homo sapiens
9606.ENSP00000296271
Belongs to the G-protein coupled receptor 1 family. Opsin subfamily.
RP4;OPN2;CSNBAD1
GO:0046872;GO:0004930;GO:0008020;GO:0005502
GO:0016021;GO:0005886;GO:0000139;GO:0005887;GO:0005794;GO:0005911;GO:0001750;GO:0097381;GO:0060170;GO:0030660;GO:0001917;GO:0060342;GO:0042622
GO:0007186;GO:0001523;GO:0018298;GO:0006468;GO:0007601;GO:0016038;GO:0045494;GO:0007603;GO:0022400;GO:0060041;GO:0016056
PhysiologyColor vision (blue-shift)Cichlid fishes; shallow watersCichlid fishes; deep waters319095African cichlidsno rank
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea; Percomorphaceae; Ovalentaria; Cichlomorphae; Cichliformes; Cichlidae
0319095African cichlidsno rank
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea; Percomorphaceae; Ovalentaria; Cichlomorphae; Cichliformes; Cichlidae
0
Data not curated
InterspecificCandidate Gene
A292S and reversals; many independent cases
CodingNo
Nonsynonymous
AugusteGCN874TCN1transversionAla292SerSNP
Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi.
Many examples of the appearance of similar traits in different lineages are known during the evolution of organisms. However; the underlying genetic mechanisms have been elucidated in very few cases. Here; we provide a clear example of evolutionary parallelism; involving changes in the same genetic pathway; providing functional adaptation of RH1 pigments to deep-water habitats during the adaptive radiation of East African cichlid fishes. We determined the RH1 sequences from 233 individual cichlids. The reconstruction of cichlid RH1 pigments with 11-cis-retinal from 28 sequences showed that the absorption spectra of the pigments of nine species were shifted toward blue; tuned by two particular amino acid replacements. These blue-shifted RH1 pigments might have evolved as adaptations to the deep-water photic environment. Phylogenetic evidence indicates that one of the replacements; A292S; has evolved several times independently; inducing similar functional change. The parallel evolution of the same mutation at the same amino acid position suggests that the number of genetic changes underlying the appearance of similar traits in cichlid diversification may be fewer than previously expected.
200515809435,1
https://sci-hub.tw/10.1073/pnas.0405302102
21172834,1
57
GP00000576MC1RMartinMC1RQ01726Homo sapiens
9606.ENSP00000451605
Belongs to the G-protein coupled receptor 1 family.
CMM5;MSH-R;SHEP2;MSHR
GO:0008528;GO:0004977;GO:0004980;GO:0031625
GO:0005886;GO:0005887;GO:0005622
GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914
AAP03515MorphologyColoration (coat)Chaetodipus intermediusChaetodipus intermedius38666
Chaetodipus intermedius
rock pocket mouse
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus
038666
Chaetodipus intermedius
rock pocket mousespecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus
0Taxon AIntraspecificCandidate GeneR18CCodingNo
Nonsynonymous
AugusteCGC52TGC1transitionArg18CysSNP
The genetic basis of adaptive melanism in pocket mice.
Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here; we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice; Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However; populations of dark (melanic) mice are found on dark lava; and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene; Mc1r; that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly; another melanic population of these mice on a different lava flow shows no association with Mc1r mutations; indicating that adaptive dark color has evolved independently in this species through changes at different genes.
200312704245,1
https://sci-hub.tw/10.1073/pnas.0431157100
58
GP00000577MC1RMartinMC1RQ01726Homo sapiens
9606.ENSP00000451605
Belongs to the G-protein coupled receptor 1 family.
CMM5;MSH-R;SHEP2;MSHR
GO:0008528;GO:0004977;GO:0004980;GO:0031625
GO:0005886;GO:0005887;GO:0005622
GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914
AAP03515MorphologyColoration (coat)Chaetodipus intermediusChaetodipus intermedius38666
Chaetodipus intermedius
rock pocket mouse
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus
038666
Chaetodipus intermedius
rock pocket mousespecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus
0Taxon AIntraspecificCandidate GeneR109WCodingNo
Nonsynonymous
AugusteCGG325TGG1transitionArg109TripSNP
The genetic basis of adaptive melanism in pocket mice.
Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here; we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice; Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However; populations of dark (melanic) mice are found on dark lava; and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene; Mc1r; that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly; another melanic population of these mice on a different lava flow shows no association with Mc1r mutations; indicating that adaptive dark color has evolved independently in this species through changes at different genes.
200312704245,1
https://sci-hub.tw/10.1073/pnas.0431157100
59
GP00000578MC1RMartinMC1RQ01726Homo sapiens
9606.ENSP00000451605
Belongs to the G-protein coupled receptor 1 family.
CMM5;MSH-R;SHEP2;MSHR
GO:0008528;GO:0004977;GO:0004980;GO:0031625
GO:0005886;GO:0005887;GO:0005622
GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914
AAP03515MorphologyColoration (coat)Chaetodipus intermediusChaetodipus intermedius38666
Chaetodipus intermedius
rock pocket mouse
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus
038666
Chaetodipus intermedius
rock pocket mousespecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus
0Taxon AIntraspecificCandidate GeneR160WCodingNo
Nonsynonymous
Auguste CGG478TGG1transitionArg160TripSNP
The genetic basis of adaptive melanism in pocket mice.
Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here; we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice; Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However; populations of dark (melanic) mice are found on dark lava; and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene; Mc1r; that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly; another melanic population of these mice on a different lava flow shows no association with Mc1r mutations; indicating that adaptive dark color has evolved independently in this species through changes at different genes.
200312704245,1
https://sci-hub.tw/10.1073/pnas.0431157100
60
GP00000579MC1RMartinMC1RQ01726Homo sapiens
9606.ENSP00000451605
Belongs to the G-protein coupled receptor 1 family.
CMM5;MSH-R;SHEP2;MSHR
GO:0008528;GO:0004977;GO:0004980;GO:0031625
GO:0005886;GO:0005887;GO:0005622
GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914
AAP03515MorphologyColoration (coat)Chaetodipus intermediusChaetodipus intermedius38666
Chaetodipus intermedius
rock pocket mouse
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus
038666
Chaetodipus intermedius
rock pocket mousespecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus
0Taxon AIntraspecificCandidate GeneQ233HCodingNo
Nonsynonymous
AugusteCAA699CAC3transversionGin233HisSNP
The genetic basis of adaptive melanism in pocket mice.
Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here; we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice; Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However; populations of dark (melanic) mice are found on dark lava; and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene; Mc1r; that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly; another melanic population of these mice on a different lava flow shows no association with Mc1r mutations; indicating that adaptive dark color has evolved independently in this species through changes at different genes.
200312704245,1
https://sci-hub.tw/10.1073/pnas.0431157100
61
GP00001135TRIM5alphaMartinTRIM5Q9C035Homo sapiens
9606.ENSP00000369373
Belongs to the TRIM/RBCC family.
RNF88;TRIM5alpha
GO:0042802;GO:0042803;GO:0008270;GO:0019901;GO:0030674;GO:0008329;GO:0004842
GO:0005737;GO:0005829;GO:0005634;GO:0000932
GO:0045087;GO:0043410;GO:0051092;GO:0051607;GO:0043123;GO:0032880;GO:0060333;GO:0016032;GO:0051091;GO:0002218;GO:0006914;GO:0046597;GO:1902187;GO:0070534;GO:0070206;GO:0031664
AEO45780Physiology
Pathogen resistance (retroviruses)
Old World MonkeysOld World Monkeys9527Cercopithecidae
Old World monkeys
family
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Cercopithecoidea
09527CercopithecidaeOld World monkeysfamily
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Cercopithecoidea
0
Data not curated
IntraspecificCandidate Gene
Complex a.a. substtutions with retrovirus-specific activities; under balancing selection in several species
CodingNo
Nonsynonymous
SNP
Balancing selection and the evolution of functional polymorphism in Old World monkey TRIM5alpha.
Retroviral restriction factor TRIM5alpha exhibits a high degree of sequence variation among primate species. It has been proposed that this diversity is the cumulative result of ancient; lineage-specific episodes of positive selection. Here; we describe the contribution of within-species variation to the evolution of TRIM5alpha. Sampling within two geographically distinct Old World monkey species revealed extensive polymorphism; including individual polymorphisms that predate speciation (shared polymorphism). In some instances; alleles were more closely related to orthologues of other species than to one another. Both silent and nonsynonymous changes clustered in two domains. Functional assays revealed consequences of polymorphism; including differential restriction of a small panel of retroviruses by very similar alleles. Together; these features indicate that the primate TRIM5alpha locus has evolved under balancing selection. Except for the MHC there are few; if any; examples of long-term balancing selection in primates. Our results suggest a complex evolutionary scenario; in which fixation of lineage-specific adaptations is superimposed on a subset of critical polymorphisms that predate speciation events and have been maintained by balancing selection for millions of years.
200617142324,1
https://sci-hub.tw/10.1073/pnas.0605838103
@& @BalancingSelection
62
GP00001191
VRS1 = SIX-ROWED SPIKE 1
MartinVrs1A1IHK8
Hordeum vulgare subsp. vulgare
Hox1GO:0043565GO:0005634GO:0006355
Morphology &2 Morphology
Plant architecture &2 Inflorescence architecture
Hordeum vulgare &2 Hordeum vulgare &2 4513Hordeum vulgarespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Triticodae; Triticeae; Hordeinae; Hordeum
04513Hordeum vulgarespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Triticodae; Triticeae; Hordeinae; Hordeum
0
Data not curated
DomesticatedLinkage MappingPhe75LeuCodingNo
Nonsynonymous
MariamTTYndYTR,CTNSNP
Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene.
Increased seed production has been a common goal during the domestication of cereal crops; and early cultivators of barley (Hordeum vulgare ssp. vulgare) selected a phenotype with a six-rowed spike that stably produced three times the usual grain number. This improved yield established barley as a founder crop for the Near Eastern Neolithic civilization. The barley spike has one central and two lateral spikelets at each rachis node. The wild-type progenitor (H. vulgare ssp. spontaneum) has a two-rowed phenotype; with additional; strictly rudimentary; lateral rows; this natural adaptation is advantageous for seed dispersal after shattering. Until recently; the origin of the six-rowed phenotype remained unknown. In the present study; we isolated vrs1 (six-rowed spike 1); the gene responsible for the six-rowed spike in barley; by means of positional cloning. The wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain with a closely linked leucine zipper motif. Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes; suggesting that the VRS1 protein suppresses development of the lateral rows. Loss of function of Vrs1 resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype. Phylogenetic analysis demonstrated that the six-rowed phenotype originated repeatedly; at different times and in different regions; through independent mutations of Vrs1.
200717220272,1
https://sci-hub.tw/10.1073/pnas.0608580104
21217754,1
63
GP00000769
opsin - rhodopsin (LWRh)
MartinLWRhE2DZP1
Heliconius melpomene
Belongs to the G-protein coupled receptor 1 family. Opsin subfamily.
BCP;BOP;CBTGO:0004930;GO:0009881GO:0016021
GO:0018298;GO:0007601;GO:0007602
AF385332PhysiologyColor vision (blue shift)
Limenitis astyanax; other butterflies
Limenitis weidemeyerii; L. archippus; L. lorquini
124411Limenitis arthemiswhite admiralspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea; Nymphalidae; Limenitidinae; Limenitidini; Limenitis
042270Limenitis archippusviceroyspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea; Nymphalidae; Limenitidinae; Limenitidini; Limenitis
0
Data not curated
Intergeneric or Higher
Candidate Gene
I17M; S137A=S180A in human LWS/MWS numbering system
CodingNo
Nonsynonymous
SNP
Adaptive evolution of color vision as seen through the eyes of butterflies.
Butterflies and primates are interesting for comparative color vision studies; because both have evolved middle- (M) and long-wavelength- (L) sensitive photopigments with overlapping absorbance spectrum maxima (lambda(max) values). Although positive selection is important for the maintenance of spectral variation within the primate pigments; it remains an open question whether it contributes similarly to the diversification of butterfly pigments. To examine this issue; we performed epimicrospectrophotometry on the eyes of five Limenitis butterfly species and found a 31-nm range of variation in the lambda(max) values of the L-sensitive photopigments (514-545 nm). We cloned partial Limenitis L opsin gene sequences and found a significant excess of replacement substitutions relative to polymorphisms among species. Mapping of these L photopigment lambda(max) values onto a phylogeny revealed two instances within Lepidoptera of convergently evolved L photopigment lineages whose lambda(max) values were blue-shifted. A codon-based maximum-likelihood analysis indicated that; associated with the two blue spectral shifts; four amino acid sites (Ile17Met; Ala64Ser; Asn70Ser; and Ser137Ala) have evolved substitutions in parallel and exhibit significant d(N)/d(S) >1. Homology modeling of the full-length Limenitis arthemis astyanax L opsin placed all four substitutions within the chromophore-binding pocket. Strikingly; the Ser137Ala substitution is in the same position as a site that in primates is responsible for a 5- to 7-nm blue spectral shift. Our data show that some of the same amino acid sites are under positive selection in the photopigments of both butterflies and primates; spanning an evolutionary distance >500 million years.
200717494749,1
https://sci-hub.tw/10.1073/pnas.0701447104
64
GP00000770
opsin - rhodopsin (LWRh)
MartinLWRhE2DZP1
Heliconius melpomene
Belongs to the G-protein coupled receptor 1 family. Opsin subfamily.
BCP;BOP;CBTGO:0004930;GO:0009881GO:0016021
GO:0018298;GO:0007601;GO:0007602
AF385332PhysiologyColor vision (blue shift)Other butterflies
Junonia coenia; Siproeta steneles
33415Nymphalidaebrushfootsfamily
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea
039707Junoniabuckeyesgenus
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea; Nymphalidae; Nymphalinae; Junoniini
0
Data not curated
Intergeneric or Higher
Candidate Gene
I17M; S137A=S180A in human LWS/MWS numbering system
CodingNo
Nonsynonymous
SNP
Adaptive evolution of color vision as seen through the eyes of butterflies.
Butterflies and primates are interesting for comparative color vision studies; because both have evolved middle- (M) and long-wavelength- (L) sensitive photopigments with overlapping absorbance spectrum maxima (lambda(max) values). Although positive selection is important for the maintenance of spectral variation within the primate pigments; it remains an open question whether it contributes similarly to the diversification of butterfly pigments. To examine this issue; we performed epimicrospectrophotometry on the eyes of five Limenitis butterfly species and found a 31-nm range of variation in the lambda(max) values of the L-sensitive photopigments (514-545 nm). We cloned partial Limenitis L opsin gene sequences and found a significant excess of replacement substitutions relative to polymorphisms among species. Mapping of these L photopigment lambda(max) values onto a phylogeny revealed two instances within Lepidoptera of convergently evolved L photopigment lineages whose lambda(max) values were blue-shifted. A codon-based maximum-likelihood analysis indicated that; associated with the two blue spectral shifts; four amino acid sites (Ile17Met; Ala64Ser; Asn70Ser; and Ser137Ala) have evolved substitutions in parallel and exhibit significant d(N)/d(S) >1. Homology modeling of the full-length Limenitis arthemis astyanax L opsin placed all four substitutions within the chromophore-binding pocket. Strikingly; the Ser137Ala substitution is in the same position as a site that in primates is responsible for a 5- to 7-nm blue spectral shift. Our data show that some of the same amino acid sites are under positive selection in the photopigments of both butterflies and primates; spanning an evolutionary distance >500 million years.
200717494749,1
https://sci-hub.tw/10.1073/pnas.0701447104
65
GP00000871phytochrome B (PHYB)MartinPHYBP14713
Arabidopsis thaliana
3702.AT2G18790.1
Belongs to the phytochrome family.
HY3;MSF3.17;MSF3_17;OOP1;OUT OF PHASE 1;phytochrome B;PHYTOCHROME B;At2g18790
GO:0042802;GO:0042803;GO:0043565;GO:0000155;GO:0031516;GO:0009883;GO:1990841;GO:0031517
GO:0005829;GO:0005634;GO:0016604;GO:0016607
GO:0009640;GO:0006351;GO:0045892;GO:0009409;GO:0006325;GO:0010617;GO:0009638;GO:0018298;GO:2000028;GO:0010244;GO:0010148;GO:0009266;GO:0010218;GO:0009867;GO:0009649;GO:0009584;GO:0009630;GO:0010161;GO:0009687;GO:0015979;GO:0017012;GO:0031347;GO:0010029;GO:0010202;GO:0010374
CP002685PhysiologyLight sensitivityArabidopsis thaliana- Ler0Arabidopsis thaliana - Cvi3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
IntraspecificLinkage MappingI143LCodingNo
Nonsynonymous
PintonATHCTH1transversionIle143LeuSNP
Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light.
Plants have a sophisticated system for sensing and responding to their light environment. The light responses of populations and species native to different habitats show adaptive variation; understanding the mechanisms underlying photomorphogenic variation is therefore of significant interest. In Arabidopsis thaliana; phytochrome B (PHYB) is the dominant photoreceptor for red light and plays a major role in white light. Because PHYB has been proposed as a candidate gene for several quantitative trait loci (QTLs) affecting light response; we have investigated sequence and functional variation in Arabidopsis PHYB. We examined PHYB sequences in 33 A. thaliana individuals and in the close relative Arabidopsis lyrata. From 14 nonsynonymous polymorphisms; we chose 5 for further study based on previous QTL studies. In a larger collection of A. thaliana accessions; one of these five polymorphisms; I143L; was associated with variation in red light response. We used transgenic analysis to test this association and confirmed experimentally that natural PHYB polymorphisms cause differential plant responses to light. Furthermore; our results show that allelic variation of PHYB activity is due to amino acid rather than regulatory changes. Together with earlier studies linking variation in light sensitivity to photoreceptor genes; our work suggests that photoreceptors may be a common target of natural selection.
200818287016,1
https://sci-hub.tw/10.1073/pnas.0712174105
@GxE
66
GP00001020S5MartinGRXS5Q5QLR2
Oryza sativa subsp. japonica
39947.LOC_Os01g47760.1
Belongs to the glutaredoxin family. CC-type subfamily.
GRXS5;P0014E08.2;Os01g0667900;LOC_Os01g47760;OSJNBb0063G05.32
GO:0046872;GO:0009055;GO:0051537;GO:0015035
GO:0005737;GO:0005634GO:0045454ACG76112Physiology
Hybrid incompatibility (F1 female sterility)
Oryza sativa japonicaOryza sativa indica4530Oryza sativaricespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
14530Oryza sativaricespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
1
Data not curated
DomesticatedLinkage Mapping6 non-synonymous changesCodingNo
Nonsynonymous
SNP
A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice.
Hybrid sterility is a major form of postzygotic reproductive isolation. Although reproductive isolation has been a key issue in evolutionary biology for many decades in a wide range of organisms; only very recently a few genes for reproductive isolation were identified. The Asian cultivated rice (Oryza sativa L.) is divided into two subspecies; indica and japonica. Hybrids between indica and japonica varieties are usually highly sterile. A special group of rice germplasm; referred to as wide-compatibility varieties; is able to produce highly fertile hybrids when crossed to both indica and japonica. In this study; we cloned S5; a major locus for indica-japonica hybrid sterility and wide compatibility; using a map-based cloning approach. We show that S5 encodes an aspartic protease conditioning embryo-sac fertility. The indica (S5-i) and japonica (S5-j) alleles differ by two nucleotides. The wide compatibility gene (S5-n) has a large deletion in the N terminus of the predicted S5 protein; causing subcellular mislocalization of the protein; and thus is presumably nonfunctional. This triallelic system has a profound implication in the evolution and artificial breeding of cultivated rice. Genetic differentiation between indica and japonica would have been enforced because of the reproductive barrier caused by S5-i and S5-j; and species coherence would have been maintained by gene flow enabled by the wide compatibility gene.
200818678896,1
https://sci-hub.tw/10.1073/pnas.0804761105
@&
67
GP00000804OR7D4MartinOR7D4Q8NG98Homo sapiens
9606.ENSP00000310488
Belongs to the G-protein coupled receptor 1 family.
OR19B;hg105;OR19-7;OR19-B;OR7D4P
GO:0004930;GO:0004984GO:0016021;GO:0005886GO:0007186;GO:0050911ALI87882PhysiologyOlfactionHuman/Chimpanzee ancestorHomo sapiens207598Homininae
subfamily
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae
09606Homo sapienshumanspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
0
Data not curated
InterspecificCandidate GeneM273TCodingNo
Nonsynonymous
PintonATGACG2transitionMet273ThrSNP
Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates.
Odorant receptors are among the fastest evolving genes in animals. However; little is known about the functional changes of individual odorant receptors during evolution. We have recently demonstrated a link between the in vitro function of a human odorant receptor; OR7D4; and in vivo olfactory perception of 2 steroidal ligands--androstenone and androstadienone--chemicals that are shown to affect physiological responses in humans. In this study; we analyzed the in vitro function of OR7D4 in primate evolution. Orthologs of OR7D4 were cloned from different primate species. Ancestral reconstruction allowed us to reconstitute additional putative OR7D4 orthologs in hypothetical ancestral species. Functional analysis of these orthologs showed an extremely diverse range of OR7D4 responses to the ligands in various primate species. Functional analysis of the nonsynonymous changes in the Old World Monkey and Great Ape lineages revealed a number of sites causing increases or decreases in sensitivity. We found that the majority of the functionally important residues in OR7D4 were not predicted by the maximum likelihood analysis detecting positive Darwinian selection.
200919955411,1
https://sci-hub.tw/10.1073/pnas.0808378106
68
GP00000779
opsin - rhodopsin (UVRh2)
MartinUVRh2E2DZL8
Heliconius melpomene
Belongs to the G-protein coupled receptor 1 family.
GCP;GOP;OPN1MWGO:0004930GO:0016021GO:0007601;GO:0007602PhysiologyColor vision (UV-shift)Other butterfliesHeliconius spp.33415Nymphalidaebrushfootsfamily
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea
033428Heliconius pachinusspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea; Nymphalidae; Heliconiinae; Heliconiini; Heliconius
0
Data not curated
Intergeneric or Higher
Candidate Gene
T180A; Y277F (human LWS/MWS numbering system)
CodingNo
Nonsynonymous
CortierMetSNP
Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies.
The butterfly Heliconius erato can see from the UV to the red part of the light spectrum with color vision proven from 440 to 640 nm. Its eye is known to contain three visual pigments; rhodopsins; produced by an 11-cis-3-hydroxyretinal chromophore together with long wavelength (LWRh); blue (BRh) and UV (UVRh1) opsins. We now find that H. erato has a second UV opsin mRNA (UVRh2)-a previously undescribed duplication of this gene among Lepidoptera. To investigate its evolutionary origin; we screened eye cDNAs from 14 butterfly species in the subfamily Heliconiinae and found both copies only among Heliconius. Phylogeny-based tests of selection indicate positive selection of UVRh2 following duplication; and some of the positively selected sites correspond to vertebrate visual pigment spectral tuning residues. Epi-microspectrophotometry reveals two UV-absorbing rhodopsins in the H. erato eye with lambda(max) = 355 nm and 398 nm. Along with the additional UV opsin; Heliconius have also evolved 3-hydroxy-DL-kynurenine (3-OHK)-based yellow wing pigments not found in close relatives. Visual models of how butterflies perceive wing color variation indicate this has resulted in an expansion of the number of distinguishable yellow colors on Heliconius wings. Functional diversification of the UV-sensitive visual pigments may help explain why the yellow wing pigments of Heliconius are so colorful in the UV range compared to the yellow pigments of close relatives lacking the UV opsin duplicate.
201020133601,1
https://sci-hub.tw/10.1073/pnas.0910085107
20478921,1@&
69
GP00000953RAS1MartinRAS1O04515
Arabidopsis thaliana
3702.AT1G09950.1
F21M12.34;F21M12_34;RESPONSE TO ABA AND SALT 1;At1g09950
GO:0043565
GO:0005886;GO:0005634;GO:0005739;GO:0005789
GO:0006351CP002684
Physiology &2 Physiology
Salt tolerance &2 Abscisic acid sensitivity
Arabidopsis thaliana - Sha &2 Arabidopsis thaliana- Ler0 &2 3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
IntraspecificLinkage MappingPremature stop codon; Lys>STOPCodingYesNonsensePintonTTATAA2transversionLeuSTPSNP
RAS1; a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis.
Soil salinity limits agricultural production and is a major obstacle for feeding the growing world population. We used natural genetic variation in salt tolerance among different Arabidopsis accessions to map a major quantitative trait locus (QTL) for salt tolerance and abscisic acid (ABA) sensitivity during seed germination and early seedling growth. A recombinant inbred population derived from Landsberg erecta (Ler; salt and ABA sensitive) x Shakdara (Sha; salt and ABA resistant) was used for QTL mapping. High-resolution mapping and cloning of this QTL; Response to ABA and Salt 1 (RAS1); revealed that it is an ABA- and salt stress-inducible gene and encodes a previously undescribed plant-specific protein. A premature stop codon results in a truncated RAS1 protein in Sha. Reducing the expression of RAS1 by transfer-DNA insertion in Col or RNA interference in Ler leads to decreased salt and ABA sensitivity; whereas overexpression of the Ler allele but not the Sha allele causes increased salt and ABA sensitivity. Our results suggest that RAS1 functions as a negative regulator of salt tolerance during seed germination and early seedling growth by enhancing ABA sensitivity and that its loss of function contributes to the increased salt tolerance of Sha.
201020212128,1
https://sci-hub.tw/10.1073/pnas.0910798107
70
GP00000629MC1RMartinMC1RQ01726Homo sapiens
9606.ENSP00000451605
Belongs to the G-protein coupled receptor 1 family.
CMM5;MSH-R;SHEP2;MSHR
GO:0008528;GO:0004977;GO:0004980;GO:0031625
GO:0005886;GO:0005887;GO:0005622
GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914
AAT90269MorphologyColoration (scales)Scleropus undulatusScleropus undulatus8520Sceloporus undulatusfence lizardspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera; Iguania; Phrynosomatidae; Phrynosomatinae; Sceloporus
08520
Sceloporus undulatus
fence lizardspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera; Iguania; Phrynosomatidae; Phrynosomatinae; Sceloporus
0
Data not curated
IntraspecificCandidate GeneH208YCodingNo
Nonsynonymous
PIntonCAYTAY1transitionHis208TyrSNP
Molecular and functional basis of phenotypic convergence in white lizards at White Sands.
There are many striking examples of phenotypic convergence in nature; in some cases associated with changes in the same genes. But even mutations in the same gene may have different biochemical properties and thus different evolutionary consequences. Here we dissect the molecular mechanism of convergent evolution in three lizard species with blanched coloration on the gypsum dunes of White Sands; New Mexico. These White Sands forms have rapidly evolved cryptic coloration in the last few thousand years; presumably to avoid predation. We use cell-based assays to demonstrate that independent mutations in the same gene underlie the convergent blanched phenotypes in two of the three species. Although the same gene contributes to light phenotypes in these White Sands populations; the specific molecular mechanisms leading to reduced melanin production are different. In one case; mutations affect receptor signaling and in the other; the ability of the receptor to integrate into the melanocyte membrane. These functional differences have important ramifications at the organismal level. Derived alleles in the two species show opposite dominance patterns; which in turn affect their visibility to selection and the spatial distribution of alleles across habitats. Our results demonstrate that even when the same gene is responsible for phenotypic convergence; differences in molecular mechanism can have dramatic consequences on trait expression and ultimately the adaptive trajectory.
201020080544,1
https://sci-hub.tw/10.1073/pnas.0911042107
71
GP00001121TFL1/GmTFL1MartinTFL1P93003
Arabidopsis thaliana
3702.AT5G03840.1
Belongs to the phosphatidylethanolamine-binding protein family.
MED24.6;TERMINAL FLOWER 1;TFL-1;At5g03840;F8F6_50
GO:0003712
GO:0005886;GO:0005737;GO:0005634;GO:0031982;GO:0005773
GO:0030154;GO:0009908;GO:0009910;GO:0009744;GO:0090344;GO:0006623
ABS57463PhysiologyGrowth determination habitGlycine max; Glycine soja
Glycine max (determinate growth habit)
3847Glycine maxsoybeanspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja
03847Glycine maxsoybeanspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja
0
Data not curated
DomesticatedLinkage MappingR62SCodingNo
Nonsynonymous
SantanaAGGAGT3transversionArg62SerSNP
Artificial selection for determinate growth habit in soybean.
Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit; whereas Glycine soja; the wild progenitor of soybean; is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes; when mated; produce progeny that segregate in a monogenic pattern. Here; we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1); a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene; each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype; but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However; the GmTfl1 homeolog; despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1; appears to be sub- or neo-functionalized; as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.
201020421496,1
https://sci-hub.tw/10.1073/pnas.1000088107
Information was double checked with Supp Table 1.
72
GP00001122TFL1/GmTFL1MartinTFL1P93003
Arabidopsis thaliana
3702.AT5G03840.1
Belongs to the phosphatidylethanolamine-binding protein family.
MED24.6;TERMINAL FLOWER 1;TFL-1;At5g03840;F8F6_50
GO:0003712
GO:0005886;GO:0005737;GO:0005634;GO:0031982;GO:0005773
GO:0030154;GO:0009908;GO:0009910;GO:0009744;GO:0090344;GO:0006623
ABS57463PhysiologyGrowth determination habitGlycine max; Glycine soja
Glycine max (determinate growth habit)
3847Glycine maxsoybeanspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja
03847Glycine maxsoybeanspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja
0
Data not curated
DomesticatedCandidate GeneP113LCodingNo
Nonsynonymous
PIntonCCTCTT2transitionPro113LeuSNP
Artificial selection for determinate growth habit in soybean.
Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit; whereas Glycine soja; the wild progenitor of soybean; is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes; when mated; produce progeny that segregate in a monogenic pattern. Here; we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1); a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene; each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype; but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However; the GmTfl1 homeolog; despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1; appears to be sub- or neo-functionalized; as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.
201020421496,1
https://sci-hub.tw/10.1073/pnas.1000088107
Information was double checked with Supp Table 1.
73
GP00001123TFL1/GmTFL1MartinTFL1P93003
Arabidopsis thaliana
3702.AT5G03840.1
Belongs to the phosphatidylethanolamine-binding protein family.
MED24.6;TERMINAL FLOWER 1;TFL-1;At5g03840;F8F6_50
GO:0003712
GO:0005886;GO:0005737;GO:0005634;GO:0031982;GO:0005773
GO:0030154;GO:0009908;GO:0009910;GO:0009744;GO:0090344;GO:0006623
ABS57463PhysiologyGrowth determination habitGlycine max; Glycine soja
Glycine max (determinate growth habit)
3847Glycine maxsoybeanspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja
03847Glycine maxsoybeanspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja
0
Data not curated
DomesticatedCandidate GeneR130KCodingNo
Nonsynonymous
PintonAGAAAA2transitionArg130LysSNP
Artificial selection for determinate growth habit in soybean.
Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit; whereas Glycine soja; the wild progenitor of soybean; is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes; when mated; produce progeny that segregate in a monogenic pattern. Here; we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1); a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene; each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype; but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However; the GmTfl1 homeolog; despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1; appears to be sub- or neo-functionalized; as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.
201020421496,1
https://sci-hub.tw/10.1073/pnas.1000088107
Information was double checked with Supp Table 1.
74
GP00001124TFL1/GmTFL1MartinTFL1P93003
Arabidopsis thaliana
3702.AT5G03840.1
Belongs to the phosphatidylethanolamine-binding protein family.
MED24.6;TERMINAL FLOWER 1;TFL-1;At5g03840;F8F6_50
GO:0003712
GO:0005886;GO:0005737;GO:0005634;GO:0031982;GO:0005773
GO:0030154;GO:0009908;GO:0009910;GO:0009744;GO:0090344;GO:0006623
ABS57463PhysiologyGrowth determination habitGlycine max; Glycine soja
Glycine max (determinate growth habit)
3847Glycine maxsoybeanspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja
03847Glycine maxsoybeanspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja
0
Data not curated
DomesticatedCandidate GeneR166WCodingNo
Nonsynonymous
MidounAGGTGG1transversionArg166TrpSNP
Artificial selection for determinate growth habit in soybean.
Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit; whereas Glycine soja; the wild progenitor of soybean; is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes; when mated; produce progeny that segregate in a monogenic pattern. Here; we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1); a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene; each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype; but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However; the GmTfl1 homeolog; despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1; appears to be sub- or neo-functionalized; as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.
201020421496,1
https://sci-hub.tw/10.1073/pnas.1000088107
Information was double checked with Supp Table 1.
75
GP00000103ARHGAP15MartinArhgap15Q811M1Mus musculus
10090.ENSMUSP00000056461
5830480G12RikGO:0005096GO:0005737;GO:0016020GO:0007165;GO:0008360AAI34461Physiology
Pathogen resistance (Trypanosoma)
Bos indicus (zebu) ; other breeds
Bos taurus (N'dama breed)9903Bosoxen; cattlegenus
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae
09913Bos tauruscattlespecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bos
1
Data not curated
IntraspecificLinkage MappingH282PCodingNo
Nonsynonymous
MidounCAYCCNHis282ProSNP
Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection.
African bovine trypanosomiasis caused by Trypanosoma sp.; is a major constraint on cattle productivity in sub-Saharan Africa. Some African Bos taurus breeds are highly tolerant of infection; but the potentially more productive Bos indicus zebu breeds are much more susceptible. Zebu cattle are well adapted for plowing and haulage; and increasing their tolerance of trypanosomiasis could have a major impact on crop cultivation as well as dairy and beef production. We used three strategies to obtain short lists of candidate genes within QTL that were previously shown to regulate response to infection. We analyzed the transcriptomes of trypanotolerant N'Dama and susceptible Boran cattle after infection with Trypanosoma congolense. We sequenced EST libraries from these two breeds to identify polymorphisms that might underlie previously identified quantitative trait loci (QTL); and we assessed QTL regions and candidate loci for evidence of selective sweeps. The scan of the EST sequences identified a previously undescribed polymorphism in ARHGAP15 in the Bta2 trypanotolerance QTL. The polymorphism affects gene function in vitro and could contribute to the observed differences in expression of the MAPK pathway in vivo. The expression data showed that TLR and MAPK pathways responded to infection; and the former contained TICAM1; which is within a QTL on Bta7. Genetic analyses showed that selective sweeps had occurred at TICAM1 and ARHGAP15 loci in African taurine cattle; making them strong candidates for the genes underlying the QTL. Candidate QTL genes were identified in other QTL by their expression profile and the pathways in which they participate.
201121593421,1
https://sci-hub.tw/10.1073/pnas.1013486108
76
GP00001027Sd1 (=GA20ox-2)Martin20ox2Q0JH50
Oryza sativa subsp. japonica
39947.LOC_Os01g66100.1
Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily.
sd1;GA20;Sd-1;20ox2;C20ox2;SD1-2E;Os20ox2;osGA20ox2;Os01g0883800;LOC_Os01g66100;B1065E10.46
GO:0046872;GO:0016491GO:0016021;GO:0005886
GO:0006935;GO:0040024;GO:0007606;GO:0050893
AER45908MorphologyPlant size (height)Oryza indica - Kasalath
Oryza sativa japonica - Nipponbare
4530Oryza sativaricespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
14530Oryza sativaricespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
1
Data not curated
DomesticatedLinkage MappingG100E + R340QCodingNo
Nonsynonymous
Codon-Taxon-A
Codon-Position
Codon-TaxonB
Codon-Site
transition-transversion
AminoAcid-Taxon A
AA-Position
AminoAcid-Taxon B
SNP
Artificial selection for a green revolution gene during japonica rice domestication.
The semidwarf phenotype has been extensively selected during modern crop breeding as an agronomically important trait. Introduction of the semidwarf gene; semi-dwarf1 (sd1); which encodes a gibberellin biosynthesis enzyme; made significant contributions to the "green revolution" in rice (Oryza sativa L.). Here we report that SD1 was involved not only in modern breeding including the green revolution; but also in early steps of rice domestication. We identified two SNPs in O. sativa subspecies (ssp.) japonica SD1 as functional nucleotide polymorphisms (FNPs) responsible for shorter culm length and low gibberellin biosynthetic activity. Genetic diversity analysis among O. sativa ssp. japonica and indica; along with their wild ancestor O. rufipogon Griff; revealed that these FNPs clearly differentiate the japonica landrace and O. rufipogon. We also found a dramatic reduction in nucleotide diversity around SD1 only in the japonica landrace; not in the indica landrace or O. rufipogon. These findings indicate that SD1 has been subjected to artificial selection in rice evolution and that the FNPs participated in japonica domestication; suggesting that ancient humans already used the green revolution gene.
201121646530,1
https://sci-hub.tw/10.1073/pnas.1019490108
@&
77
GP00000931
PRR37 pseudoresponse regulator protein 37 (SbPRR37)
MartinPRR37Q0D3B6
Oryza sativa subsp. japonica
39947.LOC_Os07g49460.1
Belongs to the ARR-like family.
PRR37;OsPRR37;DTH7;HD2;Os07g0695100;LOC_Os07g49460;P0627E10.21
GO:0042803;GO:0046872;GO:0017046;GO:0042978;GO:0004925
GO:0005634
GO:0006355;GO:0006351;GO:0009908;GO:0000160;GO:0009585;GO:0048579;GO:0048511
AGN92469PhysiologyFlowering timeSorghum bicolorSorghum bicolor- ATx6234558Sorghum bicolorsorghumspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
04113Solanum tuberosumpotatospecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
1
Data not curated
DomesticatedLinkage MappingK162N + G270*CodingYesNonsenseFayollasSNP
Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum.
Optimal flowering time is critical to the success of modern agriculture. Sorghum is a short-day tropical species that exhibits substantial photoperiod sensitivity and delayed flowering in long days. Genotypes with reduced photoperiod sensitivity enabled sorghum's utilization as a grain crop in temperate zones worldwide. In the present study; Ma(1); the major repressor of sorghum flowering in long days; was identified as the pseudoresponse regulator protein 37 (PRR37) through positional cloning and analysis of SbPRR37 alleles that modulate flowering time in grain and energy sorghum. Several allelic variants of SbPRR37 were identified in early flowering grain sorghum germplasm that contain unique loss-of-function mutations. We show that in long days SbPRR37 activates expression of the floral inhibitor CONSTANS and represses expression of the floral activators Early Heading Date 1; FLOWERING LOCUS T; Zea mays CENTRORADIALIS 8; and floral induction. Expression of SbPRR37 is light dependent and regulated by the circadian clock; with peaks of RNA abundance in the morning and evening in long days. In short days; the evening-phase expression of SbPRR37 does not occur due to darkness; allowing sorghum to flower in this photoperiod. This study provides insight into an external coincidence mechanism of photoperiodic regulation of flowering time mediated by PRR37 in the short-day grass sorghum and identifies important alleles of SbPRR37 that are critical for the utilization of this tropical grass in temperate zone grain and bioenergy production.
201121930910,1
https://sci-hub.tw/10.1073/pnas.1106212108
78
GP00000932
PRR37 pseudoresponse regulator protein 37 (SbPRR37)
MartinPRR37Q0D3B6
Oryza sativa subsp. japonica
39947.LOC_Os07g49460.1
Belongs to the ARR-like family.
PRR37;OsPRR37;DTH7;HD2;Os07g0695100;LOC_Os07g49460;P0627E10.21
GO:0042803;GO:0046872;GO:0017046;GO:0042978;GO:0004925
GO:0005634
GO:0006355;GO:0006351;GO:0009908;GO:0000160;GO:0009585;GO:0048579;GO:0048511
AGN92469PhysiologyFlowering timeSorghum bicolor
Sorghum bicolor- Blackhull Kafir
4558Sorghum bicolorsorghumspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
04113Solanum tuberosumpotatospecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
1
Data not curated
DomesticatedLinkage MappingK162NCodingNo
Nonsynonymous
FayollasAAR162AAY3transversionLys162AsnSNP
Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum.
Optimal flowering time is critical to the success of modern agriculture. Sorghum is a short-day tropical species that exhibits substantial photoperiod sensitivity and delayed flowering in long days. Genotypes with reduced photoperiod sensitivity enabled sorghum's utilization as a grain crop in temperate zones worldwide. In the present study; Ma(1); the major repressor of sorghum flowering in long days; was identified as the pseudoresponse regulator protein 37 (PRR37) through positional cloning and analysis of SbPRR37 alleles that modulate flowering time in grain and energy sorghum. Several allelic variants of SbPRR37 were identified in early flowering grain sorghum germplasm that contain unique loss-of-function mutations. We show that in long days SbPRR37 activates expression of the floral inhibitor CONSTANS and represses expression of the floral activators Early Heading Date 1; FLOWERING LOCUS T; Zea mays CENTRORADIALIS 8; and floral induction. Expression of SbPRR37 is light dependent and regulated by the circadian clock; with peaks of RNA abundance in the morning and evening in long days. In short days; the evening-phase expression of SbPRR37 does not occur due to darkness; allowing sorghum to flower in this photoperiod. This study provides insight into an external coincidence mechanism of photoperiodic regulation of flowering time mediated by PRR37 in the short-day grass sorghum and identifies important alleles of SbPRR37 that are critical for the utilization of this tropical grass in temperate zone grain and bioenergy production.
201121930910,1
https://sci-hub.tw/10.1073/pnas.1106212108
79
GP00000729SCN4A (Nav1.4)MartinSCN4AP35499Homo sapiens
9606.ENSP00000396320
Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.4/SCN4A subfamily.
HYPP;SkM1;CMS16;HYKPP;NAC1A;HOKPP2;Nav1.4;Na(V)1.4
GO:0005244;GO:0005248GO:0005887;GO:0001518
GO:0006814;GO:0019228;GO:0034765;GO:0086010;GO:0006936
AFD23228PhysiologyXenobiotic resistance (TTX)Amphiesma vibakariAmphiesma pryeri1159329Hebius vibakariJapanese keelbackspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera; Serpentes; Colubroidea; Colubridae; Natricinae; Hebius
01159330Hebius pryeriPryer's keelbackspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera; Serpentes; Colubroidea; Colubridae; Natricinae; Hebius
0Taxon AInterspecificCandidate GeneD1227E = D945E in DIII domainCodingNo
Nonsynonymous
SNP
Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes.
Natural selection often produces convergent changes in unrelated lineages; but the degree to which such adaptations occur via predictable genetic paths is unknown. If only a limited subset of possible mutations is fixed in independent lineages; then it is clear that constraint in the production or function of molecular variants is an important determinant of adaptation. We demonstrate remarkably constrained convergence during the evolution of resistance to the lethal poison; tetrodotoxin; in six snake species representing three distinct lineages from around the globe. Resistance-conferring amino acid substitutions in a voltage-gated sodium channel; Na(v)1.4; are clustered in only two regions of the protein; and a majority of the replacements are confined to the same three positions. The observed changes represent only a small fraction of the experimentally validated mutations known to increase Na(v)1.4 resistance to tetrodotoxin. These results suggest that constraints resulting from functional tradeoffs between ion channel function and toxin resistance led to predictable patterns of evolutionary convergence at the molecular level. Our data are consistent with theoretical predictions and recent microcosm work that suggest a predictable path is followed during an adaptive walk along a mutational landscape; and that natural selection may be frequently constrained to produce similar genetic outcomes even when operating on independent lineages.
201222392995,1
https://sci-hub.tw/10.1073/pnas.1113468109
27291053,1
Non-null mutation. Extreme TTX resistance evolved 5 times in Nav1.4 channel; but only in lineages that had previously evolved resistance in paralogous NaV channels
80
GP00000982
resistant to methyl viologen 1 (RMV1)
MartinRMV1Q9FFL1
Arabidopsis thaliana
3702.AT5G05630.1
Belongs to the amino acid-polyamine-organocation (APC) superfamily. Polyamine:cation symporter (PHS) (TC 2.A.3.12) family.
MJJ3.2;MJJ3_2;POLYAMINE UPTAKE TRANSPORTER 3;PUT3;resistant to methyl viologen 1;At5g05630
GO:0015297;GO:0015293;GO:0015179;GO:0015203
GO:0005886;GO:0005887
GO:0009408;GO:0015839;GO:0015846
BT008298PhysiologyPolyamine uptakeArabidopsis thaliana- Col0Arabidopsis thaliana- Nos-d3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
IntraspecificLinkage MappingIle377PheCodingYesNonsenseMariamATHndTTY1
transversions
Ile377PheSNP
Natural variation in a polyamine transporter determines paraquat tolerance in Arabidopsis.
Polyamines (PAs) are ubiquitous; polycationic compounds that are essential for the growth and survival of all organisms. Although the PA-uptake system plays a key role in mammalian cancer and in plant survival; the underlying molecular mechanisms are not well understood. Here; we identified an Arabidopsis L-type amino acid transporter (LAT) family transporter; named RMV1 (resistant to methyl viologen 1); responsible for uptake of PA and its analog paraquat (PQ). The natural variation in PQ tolerance was determined in 22 Arabidopsis thaliana accessions based on the polymorphic variation of RMV1. An RMV1-GFP fusion protein localized to the plasma membrane in transformed cells. The Arabidopsis rmv1 mutant was highly resistant to PQ because of the reduction of PQ uptake activity. Uptake studies indicated that RMV1 mediates proton gradient-driven PQ transport. RMV1 overexpressing plants were hypersensitive to PA and PQ and showed elevated PA/PQ uptake activity; supporting the notion that PQ enters plant cells via a carrier system that inherently functions in PA transport. Furthermore; we demonstrated that polymorphic variation in RMV1 controls PA/PQ uptake activity. Our identification of a molecular entity for PA/PQ uptake and sensitivity provides an important clue for our understanding of the mechanism and biological significance of PA uptake.
201222492932,1
https://sci-hub.tw/10.1073/pnas.1121406109
81
GP00000820para (kdr)MartinparaP35500
Drosophila melanogaster
7227.FBpp0303597
Belongs to the sodium channel (TC 1.A.1.10) family. Para subfamily.
bas;bss;CG9907;Dmel\CG9907;DmNav;DmNav1;DmNa[[v]];DmNa[[V]];DmNa[[v]]1;l(1)14Da;l(1)ESHS48;lincRNA.S9469;Nav1;Ocd;olfD;par;sbl;sbl-1;Shu;Shudderer
GO:0005509;GO:0005244;GO:0005248;GO:0005272
GO:0005887;GO:0001518
GO:0019228;GO:0045433;GO:0001666;GO:0009612;GO:0034765;GO:0086010;GO:0035725;GO:0007638;GO:0060078
Physiology
Xenobiotic resistance (insecticide)
Anopheles gambiae
Anopheles gambiae - resistant from Kenya
7165Anopheles gambiae
African malaria mosquito
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Culicoidea; Culicidae; Anophelinae; Anopheles; Cellia; Pyretophorus; gambiae species complex
07165Anopheles gambiae
African malaria mosquito
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Culicoidea; Culicidae; Anophelinae; Anopheles; Cellia; Pyretophorus; gambiae species complex
0Taxon AIntraspecificCandidate GeneN1575YCodingNo
Nonsynonymous
MidounAAYTAYAsn1575TyrSNP
Footprints of positive selection associated with a mutation (N1575Y) in the voltage-gated sodium channel of Anopheles gambiae.
Insecticide resistance is an ideal model to study the emergence and spread of adaptative variants. In the African malaria mosquito; Anopheles gambiae; this is complemented by a strong public health rationale. In this insect; resistance to pyrethroid and DDT insecticides is strongly associated with the mutations L1014F and L1014S within the para voltage-gated sodium channel (VGSC). Across much of West Africa; 1014F frequency approaches fixation. Here; we document the emergence of a mutation; N1575Y; within the linker between domains III-IV of the VGSC. In data extending over 40 kbp of the VGSC 1575Y occurs on only a single long-range haplotype; also bearing 1014F. The 1014F-1575Y haplotype was found in both M and S molecular forms of An. gambiae in West/Central African sample sites separated by up to 2;000 km. In Burkina Faso M form; 1575Y allele frequency rose significantly from 0.053 to 0.172 between 2008 and 2010. Extended haplotype homozygosity analysis of the wild-type 1575N allele showed rapid decay of linkage disequilibrium (LD); in sharp contrast to the extended LD exhibited by 1575Y. A haplotype with long-range LD and high/increasing frequency is a classical sign of strong positive selection acting on a recent mutant. 1575Y occurs ubiquitously on a 1014F haplotypic background; suggesting that the N1575Y mutation compensates for deleterious fitness effects of 1014F and/or confers additional resistance to insecticides. Haplotypic tests of association suggest the latter: The 1014F-1575Y haplotype confers a significant additive benefit above 1014F-1575N for survival to DDT (M form P = 0.03) and permethrin (S form P = 0.003).
201222493253,1
https://sci-hub.tw/10.1073/pnas.1201475109
82
GP00000709
Na/K-ATPase alpha-subunit
Martin
K+ ATPase alpha subunit
R4ZHW8Danaus plexippus
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIC subfamily.
Na+
GO:0005524;GO:0046872;GO:0005391
GO:0016021
GO:0071383;GO:0006813;GO:0006814;GO:0071260;GO:0042493;GO:0008217;GO:0090662;GO:0030007;GO:0006883;GO:0060081;GO:0086009;GO:0031947;GO:0045822;GO:0045823;GO:0045989;GO:0010107;GO:1990573;GO:0086004;GO:0002028;GO:0002026;GO:0036376
Physiology
Xenobiotic resistance (cardiac glucosides)
Other insects
Oncopeltus fasciatus and Lygaeus kalmii
50557Insectatrue insectsclass
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda
07536Oncopeltus fasciatusmilkweed bugspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Paraneoptera; Hemiptera; Prosorrhyncha; Heteroptera; Euheteroptera; Neoheteroptera; Panheteroptera; Pentatomomorpha; Lygaeoidea; Lygaeidae; Lygaeinae; Oncopeltus
0
Data not curated
Intergeneric or Higher
Candidate Gene
Q111T + D121N + N122H +F786N + T797A on one gene copy
CodingNo
Nonsynonymous
SNP
Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na;K-ATPase.
The extent of convergent molecular evolution is largely unknown; yet is critical to understanding the genetics of adaptation. Target site insensitivity to cardenolides is a prime candidate for studying molecular convergence because herbivores in six orders of insects have specialized on these plant poisons; which gain their toxicity by blocking an essential transmembrane carrier; the sodium pump (Na;K-ATPase). We investigated gene sequences of the Na;K-ATPase α-subunit in 18 insects feeding on cardenolide-containing plants (spanning 15 genera and four orders) to screen for amino acid substitutions that might lower sensitivity to cardenolides. The replacement N122H that was previously shown to confer resistance in the monarch butterfly (Danaus plexippus) and Chrysochus leaf beetles was found in four additional species; Oncopeltus fasciatus and Lygaeus kalmii (Heteroptera; Lygaeidae); Labidomera clivicollis (Coleoptera; Chrysomelidae); and Liriomyza asclepiadis (Diptera; Agromyzidae). Thus; across 300 Myr of insect divergence; specialization on cardenolide-containing plants resulted in molecular convergence for an adaptation likely involved in coevolution. Our screen revealed a number of other substitutions connected to cardenolide binding in mammals. We confirmed that some of the particular substitutions provide resistance to cardenolides by introducing five distinct constructs of the Drosophila melanogaster gene into susceptible eucaryotic cells under an ouabain selection regime. These functional assays demonstrate that combined substitutions of Q(111) and N(122) are synergistic; with greater than twofold higher resistance than either substitution alone and >12-fold resistance over the wild type. Thus; even across deep phylogenetic branches; evolutionary degrees of freedom seem to be limited by physiological constraints; such that the same molecular substitutions confer adaptation.
201222826239,1
https://sci-hub.tw/10.1073/pnas.1202111109
23019645,1@&
83
GP00000710
Na/K-ATPase alpha-subunit
Martin
K+ ATPase alpha subunit
R4ZHW8Danaus plexippus
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIC subfamily.
Na+
GO:0005524;GO:0046872;GO:0005391
GO:0016021
GO:0071383;GO:0006813;GO:0006814;GO:0071260;GO:0042493;GO:0008217;GO:0090662;GO:0030007;GO:0006883;GO:0060081;GO:0086009;GO:0031947;GO:0045822;GO:0045823;GO:0045989;GO:0010107;GO:1990573;GO:0086004;GO:0002028;GO:0002026;GO:0036376
Physiology
Xenobiotic resistance (cardiac glucosides)
Other insectsLabidomera clivicollis50557Insectatrue insectsclass
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda
0131652Labidomera clivicollisspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Coleoptera; Polyphaga; Cucujiformia; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Doryphorini; Labidomera
0
Data not curated
InterspecificCandidate GeneQ111V + N122HCodingNo
Nonsynonymous
SNP
Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na;K-ATPase.
The extent of convergent molecular evolution is largely unknown; yet is critical to understanding the genetics of adaptation. Target site insensitivity to cardenolides is a prime candidate for studying molecular convergence because herbivores in six orders of insects have specialized on these plant poisons; which gain their toxicity by blocking an essential transmembrane carrier; the sodium pump (Na;K-ATPase). We investigated gene sequences of the Na;K-ATPase α-subunit in 18 insects feeding on cardenolide-containing plants (spanning 15 genera and four orders) to screen for amino acid substitutions that might lower sensitivity to cardenolides. The replacement N122H that was previously shown to confer resistance in the monarch butterfly (Danaus plexippus) and Chrysochus leaf beetles was found in four additional species; Oncopeltus fasciatus and Lygaeus kalmii (Heteroptera; Lygaeidae); Labidomera clivicollis (Coleoptera; Chrysomelidae); and Liriomyza asclepiadis (Diptera; Agromyzidae). Thus; across 300 Myr of insect divergence; specialization on cardenolide-containing plants resulted in molecular convergence for an adaptation likely involved in coevolution. Our screen revealed a number of other substitutions connected to cardenolide binding in mammals. We confirmed that some of the particular substitutions provide resistance to cardenolides by introducing five distinct constructs of the Drosophila melanogaster gene into susceptible eucaryotic cells under an ouabain selection regime. These functional assays demonstrate that combined substitutions of Q(111) and N(122) are synergistic; with greater than twofold higher resistance than either substitution alone and >12-fold resistance over the wild type. Thus; even across deep phylogenetic branches; evolutionary degrees of freedom seem to be limited by physiological constraints; such that the same molecular substitutions confer adaptation.
201222826239,1
https://sci-hub.tw/10.1073/pnas.1202111109
23019645,1@&
84
GP00000711
Na/K-ATPase alpha-subunit
Martin
K+ ATPase alpha subunit
R4ZHW8Danaus plexippus
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIC subfamily.
Na+
GO:0005524;GO:0046872;GO:0005391
GO:0016021
GO:0071383;GO:0006813;GO:0006814;GO:0071260;GO:0042493;GO:0008217;GO:0090662;GO:0030007;GO:0006883;GO:0060081;GO:0086009;GO:0031947;GO:0045822;GO:0045823;GO:0045989;GO:0010107;GO:1990573;GO:0086004;GO:0002028;GO:0002026;GO:0036376
Physiology
Xenobiotic resistance (cardiac glucosides)
Other insectsLiriomyza asclepiadis50557Insectatrue insectsclass
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda
01200980
Liriomyza asclepiadis
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha; Eremoneura; Cyclorrhapha; Schizophora; Acalyptratae; Opomyzoidea; Agromyzidae; Phytomyzinae; Liriomyza
0
Data not curated
InterspecificCandidate GeneN122HCodingNo
Nonsynonymous
MidounAAYCAYAsn122HisSNP
Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na;K-ATPase.
The extent of convergent molecular evolution is largely unknown; yet is critical to understanding the genetics of adaptation. Target site insensitivity to cardenolides is a prime candidate for studying molecular convergence because herbivores in six orders of insects have specialized on these plant poisons; which gain their toxicity by blocking an essential transmembrane carrier; the sodium pump (Na;K-ATPase). We investigated gene sequences of the Na;K-ATPase α-subunit in 18 insects feeding on cardenolide-containing plants (spanning 15 genera and four orders) to screen for amino acid substitutions that might lower sensitivity to cardenolides. The replacement N122H that was previously shown to confer resistance in the monarch butterfly (Danaus plexippus) and Chrysochus leaf beetles was found in four additional species; Oncopeltus fasciatus and Lygaeus kalmii (Heteroptera; Lygaeidae); Labidomera clivicollis (Coleoptera; Chrysomelidae); and Liriomyza asclepiadis (Diptera; Agromyzidae). Thus; across 300 Myr of insect divergence; specialization on cardenolide-containing plants resulted in molecular convergence for an adaptation likely involved in coevolution. Our screen revealed a number of other substitutions connected to cardenolide binding in mammals. We confirmed that some of the particular substitutions provide resistance to cardenolides by introducing five distinct constructs of the Drosophila melanogaster gene into susceptible eucaryotic cells under an ouabain selection regime. These functional assays demonstrate that combined substitutions of Q(111) and N(122) are synergistic; with greater than twofold higher resistance than either substitution alone and >12-fold resistance over the wild type. Thus; even across deep phylogenetic branches; evolutionary degrees of freedom seem to be limited by physiological constraints; such that the same molecular substitutions confer adaptation.
201222826239,1
https://sci-hub.tw/10.1073/pnas.1202111109
85
GP00000749
Odorant receptor 3 (OR3)
MartinOR3D3J5H6Ostrinia nubilalis
Belongs to the insect chemoreceptor superfamily. Heteromeric odorant receptor channel (TC 1.A.69) family.
p;D7Nic1;p<cas>;D7H15S12;D7Icr28RN;P
GO:0005549;GO:0004984GO:0016021;GO:0005886GO:0007165AFK30395Behavior
Olfactory behavior (pheromone)
Ostrinia nubilalisOstrinia furnacalis29057Ostrinia nubilalis
European corn borer
species
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Pyraloidea; Crambidae; Pyraustinae; Ostrinia
093504Ostrinia furnacalisAsian corn borerspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Pyraloidea; Crambidae; Pyraustinae; Ostrinia
0
Data not curated
InterspecificCandidate GeneA148TCodingNo
Nonsynonymous
PintonGCNACN1transitionAla148ThrSNP
Single mutation to a sex pheromone receptor provides adaptive specificity between closely related moth species.
Sex pheromone communication; acting as a prezygotic barrier to mating; is believed to have contributed to the speciation of moths and butterflies in the order Lepidoptera. Five decades after the discovery of the first moth sex pheromone; little is known about the molecular mechanisms that underlie the evolution of pheromone communication between closely related species. Although Asian and European corn borers (ACB and ECB) can be interbred in the laboratory; they are behaviorally isolated from mating naturally by their responses to subtly different sex pheromone isomers; (E)-12- and (Z)-12-tetradecenyl acetate and (E)-11- and (Z)-11-tetradecenyl acetate (ACB: E12; Z12; ECB; E11; Z11). Male moth olfactory systems respond specifically to the pheromone blend produced by their conspecific females. In vitro; ECB(Z) odorant receptor 3 (OR3); a sex pheromone receptor expressed in male antennae; responds strongly to E11 but also generally to the Z11; E12; and Z12 pheromones. In contrast; we show that ACB OR3; a gene that has been subjected to positive selection (ω = 2.9); responds preferentially to the ACB E12 and Z12 pheromones. In Ostrinia species the amino acid residue corresponding to position 148 in transmembrane domain 3 of OR3 is alanine (A); except for ACB OR3 that has a threonine (T) in this position. Mutation of this residue from A to T alters the pheromone recognition pattern by selectively reducing the E11 response ∼14-fold. These results suggest that discrete mutations that narrow the specificity of more broadly responsive sex pheromone receptors may provide a mechanism that contributes to speciation.
201222891317,1
https://sci-hub.tw/10.1073/pnas.1204661109
@SexualDimorphism
86
GP00001337MC1RPrigentMC1RQ01726Homo sapiens
9606.ENSP00000451605
Belongs to the G-protein coupled receptor 1 family.
CMM5;MSH-R;SHEP2;MSHR
GO:0008528;GO:0004977;GO:0004980;GO:0031625
GO:0005886;GO:0005887;GO:0005622
GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914
MorphologyColoration (coat)Hawaiian feral pigHawaiian feral pig-black9823Sus scrofapigspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus
19825
Sus scrofa domesticus
domestic pig
subspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus; Sus scrofa
1Taxon AIntraspecificCandidate Genec.G>A p.Asp124AsnCodingNo
Nonsynonymous
PintonGAYAAY1transitionAsp124AsnSNP
Strong signatures of selection in the domestic pig genome.
Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits; including behavior; body composition; reproduction; and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig--the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1; PLAG1; and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs; most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs; carrying the Dominant white; Patch; or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.
201223151514,1
https://sci-hub.tw/10.1073/pnas.1217149109
26431999,1
the same mutation is known in European domestic pigs but happens independently in Hawaii
87
GP00000812OsPPKL1/qGL3MartinqLTG-3-1B3IWI0
Oryza sativa subsp. japonica
qGL3-1;qLTG3-1GO:0004930;GO:0004984GO:0016021;GO:0005886GO:0007186;GO:0050911AAD27631MorphologyGrain size
Oryza sativa L. ssp. indica - N643
Oryza sativa L. ssp. Japonica N411
4530Oryza sativaricespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
14530Oryza sativaricespecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
1
Data not curated
DomesticatedLinkage MappingAsp364GluCodingNo
Nonsynonymous
PintonGAYGAR3transversionAsp364GluSNP
Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice.
Grain size and shape are important components determining rice grain yield; and they are controlled by quantitative trait loci (QTLs). Here; we report the cloning and functional characterization of a major grain length QTL; qGL3; which encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1). We found a rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1. The rice genome has other two OsPPKL1 homologs; OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length; whereas OsPPKL2 as a positive regulator. The Kelch domains are essential for the OsPPKL1 biological function. Field trials showed that the application of the qgl3 allele could significantly increase grain yield in both inbred and hybrid rice varieties; due to its favorable effect on grain length; filling; and weight.
201223236132,1
https://sci-hub.tw/10.1073/pnas.1219776110
88
GP00000839para (kdr)MartinparaP35500
Drosophila melanogaster
7227.FBpp0303597
Belongs to the sodium channel (TC 1.A.1.10) family. Para subfamily.
bas;bss;CG9907;Dmel\CG9907;DmNav;DmNav1;DmNa[[v]];DmNa[[V]];DmNa[[v]]1;l(1)14Da;l(1)ESHS48;lincRNA.S9469;Nav1;Ocd;olfD;par;sbl;sbl-1;Shu;Shudderer
GO:0005509;GO:0005244;GO:0005248;GO:0005272
GO:0005887;GO:0001518
GO:0019228;GO:0045433;GO:0001666;GO:0009612;GO:0034765;GO:0086010;GO:0035725;GO:0007638;GO:0060078
Physiology
Xenobiotic resistance (insecticide)
Hyalella azteca -sensitive to pyrethroids
Hyalella azteca - resistant to pyrethroids
294128Hyalella aztecaspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Crustacea; Multicrustacea; Malacostraca; Eumalacostraca; Peracarida; Amphipoda; Senticaudata; Talitrida; Talitroidea; Hyalellidae; Hyalella
0294128Hyalella aztecaspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Crustacea; Multicrustacea; Malacostraca; Eumalacostraca; Peracarida; Amphipoda; Senticaudata; Talitrida; Talitroidea; Hyalellidae; Hyalella
0Taxon AIntraspecificCandidate GeneL925ICodingNo
Nonsynonymous
PintonATRATY3transversionLeu925IleSNP
Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean; Hyalella azteca.
Use of pesticides can have substantial nonlethal impacts on nontarget species; including driving evolutionary change; often with unknown consequences for species; ecosystems; and society. Hyalella azteca; a species complex of North American freshwater amphipods; is widely used for toxicity testing of water and sediment and has frequently shown toxicity due to pyrethroid pesticides. We demonstrate that 10 populations; 3 from laboratory cultures and 7 from California water bodies; differed by at least 550-fold in sensitivity to pyrethroids. The populations sorted into four phylogenetic groups consistent with species-level divergence. By sequencing the primary pyrethroid target site; the voltage-gated sodium channel; we show that point mutations and their spread in natural populations were responsible for differences in pyrethroid sensitivity. At least one population had both mutant and WT alleles; suggesting ongoing evolution of resistance. Although nonresistant H. azteca were susceptible to the typical neurotoxic effects of pyrethroids; gene expression analysis suggests the mode of action in resistant H. azteca was not neurotoxicity but was oxidative stress sustained only at considerably higher pyrethroid concentrations. The finding that a nontarget aquatic species has acquired resistance to pesticides used only on terrestrial pests is troubling evidence of the impact of chronic pesticide transport from land-based applications into aquatic systems. Our findings have far-reaching implications for continued uncritical use of H. azteca as a principal species for monitoring and environmental policy decisions.
201324065824,1
https://sci-hub.tw/10.1073/pnas.1302023110
89
GP00000840para (kdr)MartinparaP35500
Drosophila melanogaster
7227.FBpp0303597
Belongs to the sodium channel (TC 1.A.1.10) family. Para subfamily.
bas;bss;CG9907;Dmel\CG9907;DmNav;DmNav1;DmNa[[v]];DmNa[[V]];DmNa[[v]]1;l(1)14Da;l(1)ESHS48;lincRNA.S9469;Nav1;Ocd;olfD;par;sbl;sbl-1;Shu;Shudderer
GO:0005509;GO:0005244;GO:0005248;GO:0005272
GO:0005887;GO:0001518
GO:0019228;GO:0045433;GO:0001666;GO:0009612;GO:0034765;GO:0086010;GO:0035725;GO:0007638;GO:0060078
Physiology
Xenobiotic resistance (insecticide)
Hyalella azteca -sensitive to pyrethroids
Hyalella azteca - resistant to pyrethroids
294128Hyalella aztecaspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Crustacea; Multicrustacea; Malacostraca; Eumalacostraca; Peracarida; Amphipoda; Senticaudata; Talitrida; Talitroidea; Hyalellidae; Hyalella
0294128Hyalella aztecaspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Crustacea; Multicrustacea; Malacostraca; Eumalacostraca; Peracarida; Amphipoda; Senticaudata; Talitrida; Talitroidea; Hyalellidae; Hyalella
0Taxon AIntraspecificCandidate GeneM918LCodingNo
Nonsynonymous
PintonATGYTG1transversionMet918LeuSNP
Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean; Hyalella azteca.
Use of pesticides can have substantial nonlethal impacts on nontarget species; including driving evolutionary change; often with unknown consequences for species; ecosystems; and society. Hyalella azteca; a species complex of North American freshwater amphipods; is widely used for toxicity testing of water and sediment and has frequently shown toxicity due to pyrethroid pesticides. We demonstrate that 10 populations; 3 from laboratory cultures and 7 from California water bodies; differed by at least 550-fold in sensitivity to pyrethroids. The populations sorted into four phylogenetic groups consistent with species-level divergence. By sequencing the primary pyrethroid target site; the voltage-gated sodium channel; we show that point mutations and their spread in natural populations were responsible for differences in pyrethroid sensitivity. At least one population had both mutant and WT alleles; suggesting ongoing evolution of resistance. Although nonresistant H. azteca were susceptible to the typical neurotoxic effects of pyrethroids; gene expression analysis suggests the mode of action in resistant H. azteca was not neurotoxicity but was oxidative stress sustained only at considerably higher pyrethroid concentrations. The finding that a nontarget aquatic species has acquired resistance to pesticides used only on terrestrial pests is troubling evidence of the impact of chronic pesticide transport from land-based applications into aquatic systems. Our findings have far-reaching implications for continued uncritical use of H. azteca as a principal species for monitoring and environmental policy decisions.
201324065824,1
https://sci-hub.tw/10.1073/pnas.1302023110
90
GP00001468Rhodopsin (RH1)PrigentrhoP35359Danio rerio
7955.ENSDARP00000011562
Belongs to the G-protein coupled receptor 1 family. Opsin subfamily.
Rh;RH1;zfo2;rh1.1;zfrho;wu:fi06d11
GO:0008020;GO:0009881;GO:0005502;GO:0016918
GO:0016021;GO:0001750;GO:0097381
GO:0018298;GO:0007601;GO:0016038;GO:0016056;GO:0009583
AB290449PhysiologyColor vision (blue shift)
other teleost Percomorphaceae fishes (fugu & stickleback & medaka)
Pacific bluefin tuna1489872Percomorphaceaeno rank
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea
08238Thunnus orientalisPacific bluefin tunaspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea; Percomorphaceae; Pelagiaria; Scombriformes; Scombridae; Scombrinae; Thunnini; Thunnus
0Taxon A
Intergeneric or Higher
Candidate Genep.E122Q (G>C)CodingNo
Nonsynonymous
PintonGARGGR2transitionGlu122GlnSNP
Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.
Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values; the open-ocean lifestyle of tuna; in which effective sensing systems such as color vision are required for capture of prey; has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna; we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis); using next-generation sequencing technology. A total of 26;433 protein-coding genes were predicted from 16;802 assembled scaffolds. From these; we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS); UV-sensitive (short-wavelength sensitive 1; SWS1); blue-sensitive (SWS2); rhodopsin (RH1); and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e.; blue shift). Pacific bluefin tuna has at least five RH2 paralogs; the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover; phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus; Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1; RH2; and SWS2); which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and; thereby; could help to improve the technology to culture such fish in captivity for resource management.
201323781100,1
https://sci-hub.tw/10.1073/pnas.1302051110
Effect of the mutation demonstrated in a previous study in coelacanth
91
GP00001469
Green-sensitive opsin (RH2)
Prigentopn1mw1Q9W6A5Danio rerio
7955.ENSDARP00000001158
Belongs to the G-protein coupled receptor 1 family. Opsin subfamily.
RH2-1;rh2.1;zfgr1;grops1;rh21GO:0008020;GO:0009881GO:0016021;GO:0001750
GO:0018298;GO:0007601;GO:0007602
AB290451PhysiologyColor vision (blue shift)
other teleost Percomorphaceae fishes (fugu & stickleback)
Pacific bluefin tuna1489872Percomorphaceaeno rank
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea
08238Thunnus orientalisPacific bluefin tunaspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea; Percomorphaceae; Pelagiaria; Scombriformes; Scombridae; Scombrinae; Thunnini; Thunnus
0Taxon A
Intergeneric or Higher
Candidate Genep.E122Q (G>C) in four of five genesCodingNo
Nonsynonymous
PIntonGARGGR2transitionGlu122GlnSNP
Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.
Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values; the open-ocean lifestyle of tuna; in which effective sensing systems such as color vision are required for capture of prey; has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna; we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis); using next-generation sequencing technology. A total of 26;433 protein-coding genes were predicted from 16;802 assembled scaffolds. From these; we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS); UV-sensitive (short-wavelength sensitive 1; SWS1); blue-sensitive (SWS2); rhodopsin (RH1); and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e.; blue shift). Pacific bluefin tuna has at least five RH2 paralogs; the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover; phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus; Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1; RH2; and SWS2); which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and; thereby; could help to improve the technology to culture such fish in captivity for resource management.
201323781100,1
https://sci-hub.tw/10.1073/pnas.1302051110
by gene duplication and conversion there are 5 RH2 genes in tuna and four of which have the same substitution
92
GP00001284
Phosphate transporter PHO1
ArnoultPHO1Q8S403
Arabidopsis thaliana
3702.AT3G23430.1
Belongs to the SYG1 (TC 2.A.94) family.
ARABIDOPSIS PHOSPHATE 1;ATPHO1;phosphate 1;At3g23430;MLM24.26
GO:0000822;GO:0015114
GO:0016021;GO:0005886;GO:0000139;GO:0005794;GO:0005789;GO:0005802
GO:0016036;GO:0048016;GO:0006799
821924Morphology
Root growth (allometry of lateral roots)
Arabidopsis thaliana- 69 accessions
Arabidopsis thaliana- 69 accessions
3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
0UnknownIntraspecific
Association Mapping
histidine to tyrosine @position 8388425 in chromosome III
CodingNo
Nonsynonymous
PintonCAY8388425TAY1transitionHisTyrSNP
Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture.
Phenotypic plasticity is presumed to be involved in adaptive change toward species diversification. We thus examined how candidate genes underlying natural variation across populations might also mediate plasticity within an individual. Our implementation of an integrative "plasticity space" approach revealed that the root plasticity of a single Arabidopsis accession exposed to distinct environments broadly recapitulates the natural variation "space." Genome-wide association mapping identified the known gene PHOSPHATE 1 (PHO1) and other genes such as Root System Architecture 1 (RSA1) associated with differences in root allometry; a highly plastic trait capturing the distribution of lateral roots along the primary axis. The response of mutants in the Columbia-0 background suggests their involvement in signaling key modulators of root development including auxin; abscisic acid; and nitrate. Moreover; genotype-by-environment interactions for the PHO1 and RSA1 genes in Columbia-0 phenocopy the root allometry of other natural variants. This finding supports a role for plasticity responses in phenotypic evolution in natural environments.
201323980140,1
https://sci-hub.tw/10.1073/pnas.1305883110
@GxE - no strong demonstration of the putative causal SNP; natural variation between accessions recapitulates phenotypic plasticity in Col-0
93
GP00000117
AtGA20ox1 (=GA5=Sd1)
MartinGA20OX1Q39110
Arabidopsis thaliana
3702.AT4G25420.1
Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily.
ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420
GO:0046872;GO:0045544GO:0005737
GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826
U20872MorphologyPlant size (dwarfism)Arabidopsis thaliana - Col
Arabidopsis thaliana - dwarf accession (see manuscript)
3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
DomesticatedLinkage MappingW46*CodingYesNonsenseCourtierTGGndTGA3transitionTrp46STPSNP
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley.
Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants.
201324023067,1
https://sci-hub.tw/10.1073/pnas.1314979110
94
GP00000118
AtGA20ox1 (=GA5=Sd1)
MartinGA20OX1Q39110
Arabidopsis thaliana
3702.AT4G25420.1
Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily.
ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420
GO:0046872;GO:0045544GO:0005737
GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826
U20872MorphologyPlant size (dwarfism)Arabidopsis thaliana - Col
Arabidopsis thaliana - dwarf accession (see manuscript)
3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
DomesticatedLinkage MappingW271*CodingYesNonsenseCourtierTGGndTGA3transitionTrp271STPSNP
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley.
Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants.
201324023067,1
https://sci-hub.tw/10.1073/pnas.1314979110
95
GP00000119
AtGA20ox1 (=GA5=Sd1)
MartinGA20OX1Q39110
Arabidopsis thaliana
3702.AT4G25420.1
Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily.
ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420
GO:0046872;GO:0045544GO:0005737
GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826
U20872MorphologyPlant size (dwarfism)Arabidopsis thaliana - Col
Arabidopsis thaliana - dwarf accession (see manuscript)
3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
DomesticatedLinkage MappingE312*CodingYesNonsenseCourtierGARndTAR1transversionGlu312STPSNP
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley.
Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants.
201324023067,1
https://sci-hub.tw/10.1073/pnas.1314979110
96
GP00000120
AtGA20ox1 (=GA5=Sd1)
MartinGA20OX1Q39110
Arabidopsis thaliana
3702.AT4G25420.1
Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily.
ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420
GO:0046872;GO:0045544GO:0005737
GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826
U20872MorphologyPlant size (dwarfism)Arabidopsis thaliana - Col
Arabidopsis thaliana - dwarf accession (see manuscript)
3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
DomesticatedLinkage MappingG919ACodingNo
Nonsynonymous
KarlaGGNGCN2transversionGly919AlaSNP
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley.
Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants.
201324023067,1
https://sci-hub.tw/10.1073/pnas.1314979110
97
GP00000121
AtGA20ox1 (=GA5=Sd1)
MartinGA20OX1Q39110
Arabidopsis thaliana
3702.AT4G25420.1
Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily.
ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420
GO:0046872;GO:0045544GO:0005737
GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826
U20872MorphologyPlant size (dwarfism)Arabidopsis thaliana - Col
Arabidopsis thaliana - dwarf accession (see manuscript)
3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
DomesticatedLinkage MappingG940GCodingNo
Nonsynonymous
SNP
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley.
Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants.
201324023067,1
https://sci-hub.tw/10.1073/pnas.1314979110
98
GP00000122
AtGA20ox1 (=GA5=Sd1)
MartinGA20OX1Q39110
Arabidopsis thaliana
3702.AT4G25420.1
Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily.
ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420
GO:0046872;GO:0045544GO:0005737
GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826
U20872MorphologyPlant size (dwarfism)Arabidopsis thaliana - Col
Arabidopsis thaliana - dwarf accession (see manuscript)
3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
DomesticatedLinkage MappingC1334GCodingNo
Nonsynonymous
KarlaTGYGGN1transversionCys1334GlySNP
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley.
Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants.
201324023067,1
https://sci-hub.tw/10.1073/pnas.1314979110
99
GP00000123
AtGA20ox1 (=GA5=Sd1)
MartinGA20OX1Q39110
Arabidopsis thaliana
3702.AT4G25420.1
Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily.
ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420
GO:0046872;GO:0045544GO:0005737
GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826
U20872MorphologyPlant size (dwarfism)Arabidopsis thaliana - Col
Arabidopsis thaliana - dwarf accession (see manuscript)
3702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
13702Arabidopsis thalianathale cressspecies
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
1
Data not curated
DomesticatedLinkage MappingSplice Site mutation G742ACodingNo
Nonsynonymous
KarlaGGNGCN2transversionGly742AlaSNP
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley.
Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants.
201324023067,1
https://sci-hub.tw/10.1073/pnas.1314979110
@Splicing
100
GP00001348tyrosinase (TYR)PrigentTyrP11344Mus musculus
10090.ENSMUSP00000004770
Belongs to the tyrosinase family.
c;Oca1;skc35;albino
GO:0042803;GO:0046982;GO:0005507;GO:0004503
GO:0016021;GO:0005737;GO:0005829;GO:0005634;GO:0043231;GO:0048471;GO:0042470;GO:0033162
GO:0042438;GO:0043473;GO:0008283;GO:0033280;GO:0051591;GO:0009411;GO:0048538
MorphologyColoration (skin; eye; freckles)Human-dark pigmentationhuman-light pigmentation9606Homo sapienshumanspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
09606Homo sapienshumanspecies
cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
0Taxon AIntraspecific
Association Mapping
c. C>A p.Ser192TyrCodingNo
Nonsynonymous
KarlaTCNTAY2transversionSer192TyrSNP
Direct evidence for positive selection of skin; hair; and eye pigmentation in Europeans during the last 5;000 y.
Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways--HERC2; SLC45A2; and TYR--using allele frequency estimates from Eneolithic; Bronze Age; and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied; with point estimates of selection ranging from around 2-10% per generation. Our results provide direct evidence that strong selection favoring lighter skin; hair; and eye pigmentation has been operating in European populations over the last 5;000 y.
201424616518,1
https://sci-hub.tw/10.1073/pnas.1316513111
codominance is assumed- under positive selection in European populations
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