Gephebase-TE-compilation

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	Q	R	S	T	U	V	W	X	Y	Z	AA	AB	AC	AD	AE	AF	AG	AH	AI	AJ	AK	AL	AM	AN	AO	AP	AQ	AR	AS	AT	AU	AV	AW	AX	AY	AZ	BA	BB	BC	BD	BE	BF	BG	BH	BI	BJ	BK	BL	BM	BN	BO	BP	BQ	BR	BS	BT	BU	BV	BW	BX	BY	BZ	CA	CB	CC	CD	CE	CF	CG	CH	CI	CJ	CK	CL	CM	CN	CO	CP	CQ	CR	CS	CT	CU	CV
1	Gephe ID	GP00001078	GP00000519	GP00000898	GP00000859																																			GP00002058	GP00002054	GP00002052	GP00002051	GP00002050	GP00002049	GP00002040	GP00002038	GP00002024	GP00002020	GP00002019	GP00002006	GP00002005	GP00002004	GP00002003	GP00001998	GP00001985	GP00001967	GP00001961	GP00001940	GP00001910	GP00001870	GP00001869	GP00001868	GP00001867	GP00001833	GP00001782	GP00001718	GP00001715	GP00001619	GP00001460	GP00001459	GP00001407	GP00001399	GP00001393	GP00001208	GP00001203	GP00001202	GP00001201	GP00001200	GP00001199	GP00001198	GP00001194	GP00001193	GP00001192	GP00001165	GP00001137	GP00001136	GP00001084	GP00001050	GP00001018	GP00001017	GP00001014	GP00000947	GP00000926	GP00000754	GP00000680	GP00000528	GP00000517	GP00000481	GP00000433
2	Gene-Gephebase	Starch branching enzyme (SBEI) = rugosus (R)	Kit (type III receptor protein-tyrosine kinase)	plg-1	pericarp color1 (P1)								CHI								Amylose content																			B2	ABCA2	Pit	anthocyanin2 (an2)	CYP19A1	Rhg1	Ectodysplasin (EDA)	zic1/zic4	ebony	cyp6g1	cyp6g1	hsp70Ba	hsp70Ba	hsp70Ba	tryptophan phenylalanine hydroxylase	glycerol-3-phosphate dehydrogenase (Gpdh)	SOD1	Doublesex	yellow	enamelysin (MMP20)	cathepsin E	amylase	amylase	amylase	amylase	beta-tubulin (ben-1)	Jheh1-Jheh2-Jheh3 complex	phytoene synthase	Zmr1	OCA2	Chalcone synthase D (CHS-D)	Chalcone synthase D (CHS-D)	Cyp28d1	CG11699	GLO(T)	WntA	Waxy /GBSS	Waxy /GBSS	Waxy /GBSS	Waxy /GBSS	Waxy /GBSS	Waxy /GBSS	VvMYBA1	VvMYBA1	VvMYBA1	Vertnin (VRTN)	TRIM5alpha-CypA chimeric gene	TRIM5alpha-CypA chimeric gene	SUN	shrunken-2 (Sh2) = endosperm ADP-glucose pyrophosphorylase large subunit	Ruby	Ruby	RPS5	r1 colored1	Prolactin (deciduous Prolactin; dPRL)	opaque2 (O2)	MTH1	L6	Kit (type III receptor protein-tyrosine kinase)	HM1 = HC toxin reductase (HCTR) [possible pseudo-replicate from other Maize entry]	Ha_BtR
3	Username	Martin	Martin	Martin	Martin	WANDRÉOLETTI	WARANGER	Elodie	Emy	WOULOU <3	WAM WRACH' <3	WASPARD-BOULINC	WOSQUINOS	HECTOR	WNIAZEVA	WAGADOUGOU	WORI	WULLER		WUINTERO WOTERO	WOJAT	Steve Warry				PEYROCHE														Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Courtier	Prigent	Prigent	Prigent	Prigent	Prigent	Prigent	Courtier	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Courtier	Courtier	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Martin	Martin
4	Reference Title	The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme.	Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic cats.	Molecular basis of the copulatory plug polymorphism in Caenorhabditis elegans.	Isolation and molecular analysis of the maize P locus.	White grapes arose through the mutation of two similar and adjacent regulatory genes.	Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor.	A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar of rice (Oryza sativa).	High-oleate peanut mutants result from a MITE insertion into the FAD2 gene.	A large insertion in bHLH transcription factor BrTT8 resulting in yellow seed coat in Brassica rapa.	A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthesis in flowers, proanthocyanidin and phytomelanin pigmentation in seeds, and seed trichome formation.	Spontaneous mutations caused by a Helitron transposon, Hel-It1, in morning glory, Ipomoea tricolor.	A mutation in the rice chalcone isomerase gene causes the golden hull and internode 1 phenotype.	Parthenocarpic apple fruit production conferred by transposon insertion mutations in a MADS-box transcription factor.	Identification of a transposon-like insertion in a Glu-1 allele of wheat.	Adaptive evolution involving gene duplication and insertion of a novel Ty1/copia-like retrotransposon in soybean.	Insertion of an En/Spm-related transposable element into a floral homeotic gene DUPLICATED causes a double flower phenotype in the Japanese morning glory.	Transposition of reversed Ac element ends generates novel chimeric genes in maize	Transposition of reversed Ac element ends generates novel chimeric genes in maize	Transposon-induced inversion in Antirrhinum modifies nivea gene expression to give a novel flower color pattern under the control of cycloidearadialis.	Excision of Ds produces waxy proteins with a range of enzymatic activities.	Transposon-induced gene activation as a mechanism generating cluster shape somatic variation in grapevine	Expression level of ABERRANT PANICLE ORGANIZATION1 determines rice inflorescence form through control of cell proliferation in the meristem.	A novel retrotransposon inserted in the dominant Vrn-B1 allele confers spring growth habit in tetraploid wheat	B-Bolivia, an allele of the maize b1 gene with variable expression, contains a high copy retrotransposon-related sequence immediately upstream.	Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog.	Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm.	A transposon, Ping, is integrated into intron 4 of the DROOPING LEAF gene of rice, weakly reducing its expression and causing a mild drooping leaf phenotype.	Insertion of a transposon-like sequence in the 5'-flanking region of the YUCCA gene causes the stony hard phenotype.	The 17-kb Tam1 element of Antirrhinum majus induces a 3-bp duplication upon integration into the chalcone synthase gene.	Isolation of a Suppressor-mutator/Enhancer-like transposable element, Tpn1, from Japanese morning glory bearing variegated flowers.	Insertion of an En/Spm-related transposable element into a floral homeotic gene DUPLICATED causes a double flower phenotype in the Japanese morning glory.	Albinism due to transposable element insertion in fish.	Positional differences of intronic transposons in pAMT affect the pungency level in chili pepper through altered splicing efficiency.	OsVIN2 encodes a vacuolar acid invertase that affects grain size by altering sugar metabolism in rice.	Nested retrotransposition in the East Asian mouse genome causes the classical nonagouti mutation.	Expansion of a core regulon by transposable elements promotes Arabidopsis chemical diversity and pathogen defense.	Preferential insertion of a Ty1 LTR-retrotransposon into the A sub-genome's HD1 gene significantly correlated with the reduction in stem trichomes of tetraploid cotton.	A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour.	Transposition of a non-autonomous DNA transposon in the gene coding for a bHLH transcription factor results in a white bulb color of onions (Allium cepa L.).	Mutation of ABC transporter ABCA2 confers resistance to Bt toxin Cry2Ab in Trichoplusia ni.	Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a retrotransposon as a promoter.	A non-LTR retrotransposon activates anthocyanin biosynthesis by regulating a MYB transcription factor in Capsicum annuum.	Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken.	The rhg1-a (Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene.	The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes.	The medaka zic1/zic4 mutant provides molecular insights into teleost caudal fin evolution.	Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution.	Variation of gene expression associated with colonisation of an anthropized environment: comparison between African and European populations of Drosophila simulans.	Strong selective sweep associated with a transposon insertion in Drosophila simulans.	Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements.	Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements.	Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements.	Aberrant splicing of the Drosophila melanogaster phenylalanine hydroxylase pre-mRNA caused by the insertion of a B104/roo transposable element in the Henna locus.	Retrotransposon insertion induces an isozyme of sn-glycerol-3-phosphate dehydrogenase in Drosophila melanogaster.	Low-activity allele of copper-zinc superoxide dismutase (CuZnSOD) in Drosophila increases paraquat genotoxicity but does not affect near UV radiation damage.	Parallel evolution of Batesian mimicry supergene in two Papilio butterflies; P. polytes and P. memnon.	hobo-induced rearrangements are responsible for mutation bursts at the yellow locus in a natural population of Drosophila melanogaster.	Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales.	Loss of genes implicated in gastric function during platypus evolution. &2 Loss of genes implicated in gastric function during platypus evolution.	Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles.	A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster.	Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing; complementation and co-suppression.	Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat. &2 Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat.	Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene.	Molecular characterization of the mutable flaked allele for flower variegation in the common morning glory.	Molecular characterization of the mutable flaked allele for flower variegation in the common morning glory.	Hidden genetic variation shapes the structure of functional elements in Drosophila.	A transposable element insertion confers xenobiotic resistance in Drosophila.	Genetic architecture and evolution of the S locus supergene in Primula vulgaris.	Ancient homology underlies adaptive mimetic diversity across butterflies.	Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions.	Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions.	Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions.	Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions.	Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions.	Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions.	Retrotransposon-induced mutations in grape skin color.	Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: a quantitative trait locus to quantitative trait nucleotide integrated study.	Retrotransposon-induced mutations in grape skin color.	Identification of a second gene associated with variation in vertebral number in domestic pigs.	Chance favors a prepared genome.	Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1.	A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit.	Molecular Characterization of the Brittle-2 Gene Effect on Maize Endosperm ADPglucose Pyrophosphorylase Subunits.	Retrotransposons control fruit-specific; cold-dependent accumulation of anthocyanins in blood oranges.	Retrotransposons control fruit-specific; cold-dependent accumulation of anthocyanins in blood oranges.	A new Ac-like transposon of Arabidopsis is associated with a deletion of the RPS5 disease resistance gene.	Evolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci.	Transformation of a transposon into a derived prolactin promoter with function during human pregnancy.	Transposon tagging and molecular analysis of the maize regulatory locus opaque-2.	The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.	The L6 gene for flax rust resistance is related to the Arabidopsis bacterial resistance gene RPS2 and the tobacco viral resistance gene N.	Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic cats.	Reductase activity encoded by the HM1 disease resistance gene in maize.	Diverse cadherin mutations conferring resistance to Bacillus thuringiensis toxin Cry1Ac in Helicoverpa armigera.
5	Reference Abstract	We describe the cloning of the r (rugosus) locus of pea (Pisum sativum L.); which determines whether the seed is round or wrinkled. Wrinkled (rr) seeds lack one isoform of starch-branching enzyme (SBEI); present in round (RR or Rr) seeds. A major polymorphism in the SBEI gene between near-isogenic RR and rr lines shows 100% cosegregation with the r locus; establishing that the SBEI gene is at the r locus. An aberrant transcript for SBEI is produced in rr embryos. In rr lines the SBEI gene is interrupted by a 0.8 kb insertion that is very similar to the Ac/Ds family of transposable elements from maize. Failure to produce SBEI has complex metabolic consequences on starch; lipid; and protein biosynthesis in the seed.	The Dominant White locus (W) in the domestic cat demonstrates pleiotropic effects exhibiting complete penetrance for absence of coat pigmentation and incomplete penetrance for deafness and iris hypopigmentation. We performed linkage analysis using a pedigree segregating White to identify KIT (Chr. B1) as the feline W locus. Segregation and sequence analysis of the KIT gene in two pedigrees (P1 and P2) revealed the remarkable retrotransposition and evolution of a feline endogenous retrovirus (FERV1) as responsible for two distinct phenotypes of the W locus; Dominant White; and white spotting. A full-length (7125 bp) FERV1 element is associated with white spotting; whereas a FERV1 long terminal repeat (LTR) is associated with all Dominant White individuals. For purposes of statistical analysis; the alternatives of wild-type sequence; FERV1 element; and LTR-only define a triallelic marker. Taking into account pedigree relationships; deafness is genetically linked and associated with this marker; estimated P values for association are in the range of 0.007 to 0.10. The retrotransposition interrupts a DNAase I hypersensitive site in KIT intron 1 that is highly conserved across mammals and was previously demonstrated to regulate temporal and tissue-specific expression of KIT in murine hematopoietic and melanocytic cells. A large-population genetic survey of cats (n = 270); representing 30 cat breeds; supports our findings and demonstrates statistical significance of the FERV1 LTR and full-length element with Dominant White/blue iris (P < 0.0001) and white spotting (P < 0.0001); respectively. Copyright © 2014 David et al.	Heritable variation is the raw material for evolutionary change; and understanding its genetic basis is one of the central problems in modern biology. We investigated the genetic basis of a classic phenotypic dimorphism in the nematode Caenorhabditis elegans. Males from many natural isolates deposit a copulatory plug after mating; whereas males from other natural isolates?including the standard wild-type strain (N2 Bristol) that is used in most research laboratories?do not deposit plugs. The copulatory plug is a gelatinous mass that covers the hermaphrodite vulva; and its deposition decreases the mating success of subsequent males. We show that the plugging polymorphism results from the insertion of a retrotransposon into an exon of a novel mucin-like gene; plg-1; whose product is a major structural component of the copulatory plug. The gene is expressed in a subset of secretory cells of the male somatic gonad; and its loss has no evident effects beyond the loss of male mate-guarding. Although C. elegans descends from an obligate-outcrossing; male?female ancestor; it occurs primarily as self-fertilizing hermaphrodites. The reduced selection on male?male competition associated with the origin of hermaphroditism may have permitted the global spread of a loss-of-function mutation with restricted pleiotropy.	The maize P locus is involved in the synthesis of a red flavonoid pigment in the pericarp; cob and other floral tissues. The tissue-specific pattern of expression of certain P alleles suggests that P may be a complex locus; with more than one functional unit. The P-VV allele; which specifies variegated pericarp and variegated cob; however; shows that insertion and excision of the transposable element Ac affects both pericarp and cob expression as though cob and pericarp pigmentation are controlled by a single gene. Using Ac as a transposon tag; we have isolated 34 kb of genomic DNA from the P-VV and P-RR allele. The cloned DNA contains two 5.8 kb cross-hybridizing regions; in direct orientation relative to each other; separated by 6.6 kb of intervening DNA. A sequence motif of 250 bp is repeated at three locations within the cloned region: once within each of the 5.8 kb repeats; and once outside the 5.8 kb repeats. DNA fragments flanking the Ac element detect five transcripts in RNA from wild type (P-RR) that are absent from mutant (P-VV) tissues. To localize the transcribed sequences; DNA probes spanning the 34 kb of cloned DNA were used in Northern analysis of RNA from mutant and wild-type kernels. The results suggest the presence of a single transcriptional unit located primarily within the DNA between the 5.8 kb repeats. The five RNAs transcribed from this region may be formed by alternative splicing. The size of the P gene derived from the length of the transcribed region seems much smaller than the gene size estimated from Ac-induced P-VV mutations.			DNA polymorphism of the Wx gene in gluti-nous rice cultivars was investigated by PCR-RF-SSCP andheteroduplex cleavage analysis using Brassica petioleextract, and the nucleotide sequence variations were identi-Wed. Most japonica-type glutinous rice was found to have a23-bp duplication in the second exon, which causes loss ofthe function of granule-bound starch synthase (GBSS)encoded by the Wx gene. Without the 23-bp duplication,there was an insertion of 7,764 bp in the ninth exon of thewx allele of ‘Oragamochi’. Expression analysis of the wxallele using RT-PCR and Northern blot analysis revealedthat transcripts of the ‘Oragamochi’ wx allele are about 1-kb shorter and that the deduced amino acid sequence of thetranscript lacks a motif important for GBSS. Therefore, thisinsertion was considered to be the cause of the glutinoustrait of ‘Oragamochi’. This 7,764-bp insertion had long ter-minal repeats, a primer binding site, and a polypurine tract,but no sequence homologous with gag and pol, suggestingthat it is a non-autonomous element. Furthermore, it had astructure similar to Dasheng and may be a member ofDasheng.				Helitronsare newcomers among eukaryotic DNA transposons and have originally been identified bycomputational analysis in the genomes of Arabidopsis, rice and nematode. They are distinguished from othertransposons in their structural features, and their proposed transposition mechanisms are involved in rollingcircle replication. Computer-predicted autonomousHelitronswith conserved terminal sequences 5¢-TC andCTRR-3¢are presumed to encode a putative transposase, Rep/Hel-TPase, which contains a characteristicnuclease/ligase domain for the replication-initiation protein (Rep) and a DNA helicase domain (Hel). PlantHelitronsare thought to encode an additional transposase, RPA-TPase, which is related to the largest subunitof the replication protein A (RPA70). AlthoughHelitronsare found in diverse genomes, neither an autonomouselement nor a transposition event has been reported. Here we show that a spontaneouspearly-smutant ofIpomoea tricolorcv. Pearly Gates, exhibiting white flowers and isolated in approximately 1940, has an 11.5-kbpnovelHelitron, namedHel-It1, integrated into theDFR-Bgene for anthocyanin pigmentation.Hel-It1shows thepredicted plantHelitronstructure for an autonomous element with the conserved termini and carrying the twoputative transposase genes,Rep/Hel-TPaseandRPA-TPase, which contain a nonsense and a frameshiftmutation, respectively.Hel-It1-related elements are scattered in theIpomoeagenome, and only a fraction ofthepearly-splants were found to carryHel-It1at another insertion site. Thepearly-smutant appears to bear anautonomous element and to express the wild-typeRPA-TPasetranscripts. The structures of a putativeautonomous element and its transposase genes are discussed.Keywords:Helitron, DNA transposons, spontaneous mutations,Ipomoea, anthocyanin biosynthesis, trans-posase genes.	The biosynthesis of flavonoids, important secondary plant metabolites, has been investigated extensively, but few mutants of genes in this pathway have been identified in rice (Oryza sativa). The ricegold hull and internode(gh) mutants exhibit a reddish-brown pigmentation in the hull and internode and their phenotype has long been used as a morphological marker trait for breeding and genetic study. Here, we characterized that the gh1 mutant was a mutant of the rice chalcone isomerase gene (OsCHI). The result showed that gh1 had a Dasheng retrotransposon inserted in the 50UTR of the OsCHI gene, which resulted in the complete loss of OsCHI expression. gh1 exhibited golden pigmentation in hulls and internodes once the panicles wereexposed to light. The total flavonoid content in gh1 hulls was increased threefold compared to wild type. Consistent with the gh1 phenotype, OsCHI transcripts were expressed in most tissues of rice and most abundantly in internodes. It was also expressed at high levels in panicles before heading, distributed mainly in lemmas and paleae, but its expression decreased substantially after the panicles emerged from the sheath. OsCHI encodes a protein functionally and structurally conserved to chalcone isomerases in other species. Our findings demonstrated that the OsCHI gene was indispensable for flux of the flavonoid pathway in rice.			Gene duplication is a major force for generating evolutionary novelties that lead to adaptations to environments. We previously identified two paralogs encoding phytochrome A (phyA), GmphyA1 and GmphyA2, in soybean, a paleopolyploid species. GmphyA2 is encoded by the E4 locus responsible for photoperiod sensitivity. In photoperiod insensitive lines, GmphyA2 is inactivated by the insertion of a retrotransposon in exon 1. Here, we describe the detailed characterization of the element and its evolutionary significance inferred from the distribution of the allele that harbors the element. Structural characteristics indicated that the element, designated SORE-1, is a novel Ty1/copia-like retrotransposon in soybean, which was phylogenetically related to the Sto-4, BARE-1, and RIRE1 elements. The element was transcriptionally active, and the transcription was partially repressed by an epigenetic mechanism. Sequences homologous with SORE-1 were detected in a genome sequence database of soybean, most of which appeared silent. GmphyA2 that harbors the SORE-1 insertion was detected only in cultivated soybean lines grown in northern regions of Japan, consistent with the notion that photoperiod insensitivity caused by the dysfunction of GmphyA2 is one of genetic changes that allowed soybean cultivation at high latitudes. Taking into account that genetic redundancy is conferred by the two phyA genes, we propose a novel model for the consequences of gene duplication and transposition of retrotransposons: when the gene is duplicated, retrotransposon insertion that causes the loss of a gene function can lead to adaptive evolution while the organism is sustained by the buffering effect brought about by gene duplication.							Two types of branches, rachis branches (i.e. nonfloral) and spikelets (i.e. floral), are produced during rice (Oryza sativa) inflorescence development. We previously reported that the ABERRANT PANICLE ORGANIZATION1 (APO1) gene, encoding an F-box-containing protein orthologous to Arabidopsis (Arabidopsis thaliana) UNUSUAL FLORAL ORGANS, suppresses precocious conversion of rachis branch meristems to spikelets to ensure generation of certain number of spikelets. Here, we identified four dominant mutants producing an increased number of spikelets and found that they are gain-of-function alleles of APO1. The APO1 expression levels are elevated in all four mutants, suggesting that an increase of APO1 activity caused the delay in the program shift to spikelet formation. In agreement with this result, ectopic overexpression of APO1 accentuated the APO1 gain-of-function phenotypes. In the apo1-D dominant alleles, the inflorescence meristem starts to increase in size more vigorously than the wild type when switching to the reproductive development phase. This alteration in growth rate is opposite to what is observed with the apo1 mutants that have a smaller inflorescence meristem. The difference in meristem size is caused by different rates of cell proliferation. Collectively, these results suggest that the level of APO1 activity regulates the inflorescence form through control of cell proliferation in the meristem.																	A DNA transposon was found in the gene encoding a bHLH transcription factor. Genotypes of the marker tagging this DNA transposon perfectly co-segregated with color phenotypes in large F populations A combined approach of bulked segregant analysis and RNA-Seq was used to isolate causal gene for C locus controlling white bulb color in onions (Allium cepa L.). A total of 114 contigs containing homozygous single nucleotide polymorphisms (SNPs) between white and yellow bulked RNAs were identified. Four of them showed high homologies with loci clustered in the middle of chromosome 5. SNPs in 34 contigs were confirmed by sequencing of PCR products. One of these contigs showed perfect linkage to the C locus in F populations consisting of 2491 individuals. However; genotypes of molecular marker tagging this contig were inconsistent with color phenotypes of diverse breeding lines. A total of 146 contigs showed differential expression between yellow and white bulks. Among them; transcription levels of B2 gene encoding a bHLH transcription factor were significantly reduced in white RNA bulk and F individuals; although there was no SNP in the coding region. Phylogenetic analysis showed that onion B2 was orthologous to bHLH-coding genes regulating anthocyanin biosynthesis pathway in other plant species. Promoter regions of B2 gene were obtained by genome walking and a 577-bp non-autonomous DNA transposon designated as AcWHITE was found in the white allele. Molecular marker tagging AcWHITE showed perfect linkage with the C locus. Marker genotypes of the white allele were detected in some white accessions. However; none of tested red or yellow onions contained AcWHITE insertion; implying that B2 gene was likely to be a casual gene for the C locus.	Insecticidal proteins from Bacillus thuringiensis (Bt) are the primary recombinant proteins expressed in transgenic crops (Bt-crops) to confer insect resistance. Development of resistance to Bt toxins in insect populations threatens the sustainable application of Bt-crops in agriculture. The Bt toxin Cry2Ab is a major insecticidal protein used in current Bt-crops; and resistance to Cry2Ab has been selected in several insects; including the cabbage looper; Trichoplusia ni. In this study; the Cry2Ab resistance gene in T. ni was mapped to Chromosome 17 by genetic linkage analyses using a whole genome resequencing approach; and was then finely mapped using RNA-seq-based bulked segregant analysis (BSA) and amplicon sequencing (AmpSeq)-based fine linkage mapping to a locus containing two genes; ABCA1 and ABCA2. Mutations in ABCA1 and ABCA2 in Cry2Ab resistant T. ni were identified by both genomic DNA and cDNA sequencing. Analysis of the expression of ABCA1 and ABCA2 in T. ni larvae indicated that ABCA2 is abundantly expressed in the larval midgut; but ABCA1 is not a midgut-expressed gene. The mutation in ABCA2 in Cry2Ab resistant T. ni was identified to be an insertion of a transposon Tntransib in ABCA2. For confirmation of ABCA2 as the Cry2Ab-resistance gene; T. ni mutants with frameshift mutations in ABCA1 and ABCA2 were generated by CRISPR/Cas9 mutagenesis. Bioassays of the T. ni mutants with Cry2Ab verified that the mutations of ABCA1 did not change larval susceptibility to Cry2Ab; but the ABCA2 mutants were highly resistant to Cry2Ab. Genetic complementation test of the ABCA2 allele in Cry2Ab resistant T. ni with an ABCA2 mutant generated by CRISPR/Cas9 confirmed that the ABCA2 mutation in the Cry2Ab resistant strain confers the resistance. The results from this study confirmed that ABCA2 is essential for the toxicity of Cry2Ab in T. ni and mutation of ABCA2 confers the resistance to Cry2Ab in the resistant T. ni strain derived from a Bt resistant greenhouse population. Copyright © 2019 Elsevier Ltd. All rights reserved.	The plant genome contains a large number of disease resistance (R) genes that have evolved through diverse mechanisms. Here; we report that a long terminal repeat (LTR) retrotransposon contributed to the evolution of the rice blast resistance gene Pit. Pit confers race-specific resistance against the fungal pathogen Magnaporthe grisea; and is a member of the nucleotide-binding site leucine-rich repeat (NBS-LRR) family of R genes. Compared with the non-functional allele Pit(Npb); the functional allele Pit(K59) contains four amino acid substitutions; and has the LTR retrotransposon Renovator inserted upstream. Pathogenesis assays using chimeric constructs carrying the various regions of Pit(K59) and Pit(Npb) suggest that amino acid substitutions might have a potential effect in Pit resistance; more importantly; the upregulated promoter activity conferred by the Renovator sequence is essential for Pit function. Our data suggest that transposon-mediated transcriptional activation may play an important role in the refunctionalization of additional 'sleeping' R genes in the plant genome.	The flavonoid compound anthocyanin is an important plant metabolite with nutritional and aesthetic value as well as anti-oxidative capacity. MYB transcription factors are key regulators of anthocyanin biosynthesis in plants. In pepper (Capsicum annuum); the CaAn2 gene; encoding an R2R3 MYB transcription factor; regulates anthocyanin biosynthesis. However; no functional study or structural analysis of functional and dysfunctional CaAn2 alleles has been performed. Here; to elucidate the function of CaAn2; we generated transgenic Nicotiana benthamiana and Arabidopsis thaliana plants expressing CaAn2. All of the tissues in these plants were purple. Promoter analysis of CaAn2 in purple C. annuum 'KC00134' plants revealed the insertion of a non-long terminal repeat (LTR) retrotransposon designated Ca-nLTR-A. To determine the promoter activity and functional domain of Ca-nLTR-A; various constructs carrying different domains of Ca-nLTR-A fused with GUS were transformed into N. benthamiana. Promoter analysis showed that the 3' untranslated region (UTR) of the second open reading frame of Ca-nLTR-A is responsible for CaAn2 expression in 'KC00134'. Sequence analysis of Ca-nLTR-A identified transcription factor binding sites known to regulate anthocyanin biosynthesis. This study indicates that insertion of a non-LTR retrotransposon in the promoter may activate expression of CaAn2 by recruiting transcription factors at the 3' UTR and thus provides the first example of exaptation of a non-LTR retrotransposon into a new promoter in plants. Copyright © 2019 Elsevier B.V. All rights reserved.	Henny feathering in chickens is determined by a dominant mutation that transforms male-specific plumage to female-like plumage. Previous studies indicated that this phenotype is caused by ectopic expression in skin of CYP19A1 encoding aromatase that converts androgens to estrogen and thereby inhibits the development of male-specific plumage. A long terminal repeat (LTR) from an uncharacterized endogenous retrovirus (ERV) insertion was found in an isoform of the CYP19A1 transcript from henny feathering chicken. However; the complete sequence and the genomic position of the insertion were not determined. We used publicly available whole genome sequence data to determine the flanking sequences of the ERV; and then PCR amplified the entire insertion and sequenced it using Nanopore long reads and Sanger sequencing. The 7524 bp insertion contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains; suggesting a recent integration. The ERV 3'LTR; containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the CYP19A1 5' untranslated region; was detected partially in an aromatase transcript; which present a plausible explanation for ectopic expression of aromatase in non-ovarian tissues underlying the henny feathering phenotype. We demonstrate that the henny feathering allele harbors an insertion of an intact avian leukosis virus at the 5'end of CYP19A1. The presence of this ERV showed complete concordance with the henny feathering phenotype both within a pedigree segregating for this phenotype and across breeds.	Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance-conferring Rhg1 haplotypes are recognized: rhg1-a ("Peking-type;" low-copy number; three or fewer Rhg1 repeats) and rhg1-b ("PI 88788-type;" high-copy number; four or more Rhg1 repeats). The rhg1-a and rhg1-b haplotypes encode α-SNAP (alpha-Soluble NSF Attachment Protein) variants α-SNAP LC and α-SNAP HC; respectively; with differing atypical C-terminal domains; that contribute to SCN resistance. Here we report that rhg1-a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (α-SNAP-encoding) gene. We termed this retrotransposon "RAC;" for Rhg1 alpha-SNAP copia. Soybean carries multiple RAC-like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1-a haplotypes we tested and was not detected in any examined rhg1-b or Rhg1 (single-copy) soybeans. RAC is an intact element residing within intron 1; anti-sense to the rhg1-a α-SNAP open reading frame. RAC has intrinsic promoter activities; but overt impacts of RAC on transgenic α-SNAP LC mRNA and protein abundance were not detected. From the native rhg1-a RAC genomic context; elevated α-SNAP LC protein abundance was observed in syncytium cells; as was previously observed for α-SNAP HC (whose rhg1-b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence; just ~42% of USDA accessions bearing previously identified rhg1-a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1-a accessions lacking RAC revealed that none encoded α-SNAPLC; and thus; they are not rhg1-a. rhg1-a haplotypes are of rising interest; with Rhg4; for combating SCN populations that exhibit increased virulence against the widely used rhg1-b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci; and a selectable feature that is predictive of rhg1-a haplotypes.	Most mammals; birds; and reptiles are readily recognized by their hairs; feathers; and scales; respectively. However; the lack of fossil intermediate forms between scales and hairs and substantial differences in their morphogenesis and protein composition have fueled the controversy pertaining to their potential common ancestry for decades. Central to this debate is the apparent lack of an "anatomical placode" (that is; a local epidermal thickening characteristic of feathers' and hairs' early morphogenesis) in reptile scale development. Hence; scenarios have been proposed for the independent development of the anatomical placode in birds and mammals and parallel co-option of similar signaling pathways for their morphogenesis. Using histological and molecular techniques on developmental series of crocodiles and snakes; as well as of unique wild-type and EDA (ectodysplasin A)-deficient scaleless mutant lizards; we show for the first time that reptiles; including crocodiles and squamates; develop all the characteristics of an anatomical placode: columnar cells with reduced proliferation rate; as well as canonical spatial expression of placode and underlying dermal molecular markers. These results reveal a new evolutionary scenario where hairs; feathers; and scales of extant species are homologous structures inherited; with modification; from their shared reptilian ancestor's skin appendages already characterized by an anatomical placode and associated signaling molecules.	Teleosts have an asymmetrical caudal fin skeleton formed by the upward bending of the caudal-most portion of the body axis; the ural region. This homocercal type of caudal fin ensures powerful and complex locomotion and is regarded as one of the most important innovations for teleosts during adaptive radiation in an aquatic environment. However; the mechanisms that create asymmetric caudal fin remain largely unknown. The spontaneous medaka (teleost fish) mutant; Double anal fin (Da); exhibits a unique symmetrical caudal skeleton that resembles the diphycercal type seen in Polypterus and Coelacanth. We performed a detailed analysis of the Da mutant to obtain molecular insight into caudal fin morphogenesis. We first demonstrate that a large transposon; inserted into the enhancer region of the zic1 and zic4 genes (zic1/zic4) in Da; is associated with the mesoderm-specific loss of their transcription. We then show that zic1/zic4 are strongly expressed in the dorsal part of the ural mesenchyme and thereby induce asymmetric caudal fin development in wild-type embryos; whereas their expression is lost in Da. Comparative analysis further indicates that the dorsal mesoderm expression of zic1/zic4 is conserved in teleosts; highlighting the crucial role of zic1/zic4 in caudal fin morphogenesis. Copyright © 2012 Elsevier Ltd. All rights reserved.	Hox genes pattern the anterior-posterior axis of animals and are posited to drive animal body plan evolution; yet their precise role in evolution has been difficult to determine. Here; we identified evolutionary modifications in the Hox gene Abd-B that dramatically altered its expression along the body plan of Drosophila santomea. Abd-B is required for pigmentation in Drosophila yakuba; the sister species of D. santomea; and changes to Abd-B expression would be predicted to make large contributions to the loss of body pigmentation in D. santomea. However; manipulating Abd-B expression in current-day D. santomea does not affect pigmentation. We attribute this epistatic interaction to four other genes within the D. santomea pigmentation network; three of which have evolved expression patterns that do not respond to Abd-B. Our results demonstrate how body plans may evolve through small evolutionary steps distributed throughout Hox-regulated networks. Polygenicity and epistasis may hinder efforts to identify genes and mechanisms underlying macroevolutionary traits. Copyright © 2019 Elsevier Ltd. All rights reserved.	The comparison of transcriptome profiles among populations is a powerful tool for investigating the role of gene expression change in adaptation to new environments. In this study; we use massively parallel sequencing of 3' cDNAs obtained from large samples of adult males; to compare a population of Drosophila simulans from a natural reserve within its ancestral range (eastern Africa) with a derived population collected in the strongly anthropized Rhône valley (France). The goal was to scan for adaptation linked to the invasion of new environments by the species. Among 15;090 genes retained for the analysis; 794 were found to be differentially expressed between the two populations. We observed an increase in expression of reproduction-related genes in eastern Africa; and an even stronger increase in expression of Cytochrome P450; Glutathione transferase and Glucuronosyl transferase genes in the derived population. These three gene families are involved in detoxification processes; which suggests that pesticides are a major environmental pressure for the species in this area. The survey of the Cyp6g1 upstream region revealed the insertion of a transposable element; Juan; in the regulatory sequence that is almost fixed in the Rhône Valley; but barely present in Mayotte. This shows that Cyp6g1 has undergone parallel evolution in derived populations of D. simulans as previously shown for D. melanogaster. The increasing amount of data produced by comparative population genomics and transcriptomics should permit the identification of additional genes associated with functional divergence among those differentially expressed.	We know little about several important properties of beneficial mutations; including their mutational origin; their phenotypic effects (e.g.; protein structure changes vs. regulatory changes); and the frequency and rapidity with which they become fixed in a population. One signature of the spread of beneficial mutations is the reduction of heterozygosity at linked sites. Here; we present population genetic data from several loci across chromosome arm 2R in Drosophila simulans. A 100-kb segment from a freely recombining region of this chromosome shows extremely reduced heterozygosity in a California population sample; yet typical levels of divergence between species; suggesting that at least one episode of strong directional selection has occurred in the region. The 5' flanking sequence of one gene in this region; Cyp6g1 (a cytochrome P450); is nearly fixed for a Doc transposable element insertion. Presence of the insertion is correlated with increased transcript abundance of Cyp6g1; a phenotype previously shown to be associated with insecticide resistance in Drosophila melanogaster. Surveys of nucleotide variation in the same genomic region in an African D. simulans population revealed no evidence for a high-frequency Doc element and no evidence for reduced polymorphism. These data are consistent with the notion that the Doc element is a geographically restricted beneficial mutation. Data from D. simulans Cyp6g1 are paralleled in many respects by data from its sister species D. melanogaster.	We report multiple cases in which disruption of hsp70 regulatory regions by transposable element (TE) insertions underlies natural variation in expression of the stress-inducible molecular chaperone Hsp70 in Drosophila melanogaster. Three D. melanogaster populations from different continents are polymorphic for jockey or P element insertions in the promoter of the hsp70Ba gene. All three TE insertions are within the same 87-bp region of hsp70Ba promoter; and we suggest that the distinctive promoter architecture of hsp genes may make them vulnerable to TE insertions. Each of the TE insertions reduces Hsp70 levels; and RNase protection assays demonstrate that such insertions can reduce transcription of the hsp70Ba gene. In addition; the TEs alter two measures of organismal fitness; inducible thermotolerance and female reproductive success. Thus; transposition can create quantitative genetic variation in gene expression within populations; on which natural selection can act.	We report multiple cases in which disruption of hsp70 regulatory regions by transposable element (TE) insertions underlies natural variation in expression of the stress-inducible molecular chaperone Hsp70 in Drosophila melanogaster. Three D. melanogaster populations from different continents are polymorphic for jockey or P element insertions in the promoter of the hsp70Ba gene. All three TE insertions are within the same 87-bp region of hsp70Ba promoter; and we suggest that the distinctive promoter architecture of hsp genes may make them vulnerable to TE insertions. Each of the TE insertions reduces Hsp70 levels; and RNase protection assays demonstrate that such insertions can reduce transcription of the hsp70Ba gene. In addition; the TEs alter two measures of organismal fitness; inducible thermotolerance and female reproductive success. Thus; transposition can create quantitative genetic variation in gene expression within populations; on which natural selection can act.	We report multiple cases in which disruption of hsp70 regulatory regions by transposable element (TE) insertions underlies natural variation in expression of the stress-inducible molecular chaperone Hsp70 in Drosophila melanogaster. Three D. melanogaster populations from different continents are polymorphic for jockey or P element insertions in the promoter of the hsp70Ba gene. All three TE insertions are within the same 87-bp region of hsp70Ba promoter; and we suggest that the distinctive promoter architecture of hsp genes may make them vulnerable to TE insertions. Each of the TE insertions reduces Hsp70 levels; and RNase protection assays demonstrate that such insertions can reduce transcription of the hsp70Ba gene. In addition; the TEs alter two measures of organismal fitness; inducible thermotolerance and female reproductive success. Thus; transposition can create quantitative genetic variation in gene expression within populations; on which natural selection can act.	We report the insertion of the transposable element B104 in the Phenylalanine hydroxylase gene of the Drosophila mutant Henna-recessive 3. Its presence alters the Phenylalanine hydroxylase splicing pattern; producing at least two aberrant mRNAs which contain part of the B104 sequence interrupting the coding region. This aberrant splicing is provoked by the use of a cryptic donor site encoded by the B104 3' long terminal repeat in combination with either the gene intron 3 acceptor site or a novel acceptor site generated by the target duplication caused by transposition. One of them; referred as mRNA type 1; encodes a truncated protein that could be predictably non-functional. In mRNA type 2; in spite of a 42 nt insertion; the Phenylalanine hydroxylase reading frame is not altered and it would encode for a protein with 14 extra amino acids which would be able to account for the low enzyme activity detected in this mutant. These results demonstrated that Henna locus encodes the enzyme phenylalanine hydroxylase providing direct evidence of its participation in pteridine synthesis. Moreover; it constitutes an example of the ability of transposable elements to generate protein variation in populations with the evolutionary consequences that this implies.	The insertion of the blood retrotransposon into the untranslated region of exon 7 of the sn-glycerol-3-phosphate dehydrogenase-encoding gene (Gpdh) in Drosophila melanogaster induces a GPDH isozyme-GPDH-4-and alters the pattern of expression of the three normal isozymes-GPDH-1 to GPDH-3. The process of transcript terminus formation inside the retrotransposon insertion reduces the level of the Gpdh transcript that contains exon 8 and increases the level of the transcript that contains exons 1-7. The induced GPDH-4 isozyme is a translation product of the three transcripts that contain fragments of the blood retrotransposon. The mechanism of mutagenesis by the blood insertion is postulated to involve the pause or termination of transcription within the blood sequence; which in turn is caused by the interference of a DNA-binding protein with the RNA polymerase. Thus; we show the formation of a new functional GPDH protein by the insertion of a transposable element and discuss the evolutionary significance of this phenomenon.	Different types of mutations and DNA-damage profiles induced by near-UV radiation and the superoxide anion (O2-.) indicate separate lesions and (or) mechanisms of mutagenesis. Despite a wealth of data; it is still unclear whether variations in the activity levels of antioxidant enzymes naturally present in suboptimal concentrations are among the underlying causes of the increase of near UV radiation genotoxicity. We incorporated a low-activity allele of copper-zinc superoxide dismutase (CuZnSOD); recovered from natural populations of Drosophila melanogaster; into standard marked strains and employed a somatic mutation and recombination test (SMART) to compare paraquat and near UV radiation genotoxicity in these strains. Our results show that; although the low-activity CuZnSOD allele of D. melanogaster confers hypersensitivity to paraquat; the near UV radiation damage was not affected.	Batesian mimicry protects animals from predators when mimics resemble distasteful models. The female-limited Batesian mimicry in Papilio butterflies is controlled by a supergene locus switching mimetic and nonmimetic forms. In Papilio polytes; recent studies revealed that a highly diversified region (HDR) containing doublesex (dsx-HDR) constitutes the supergene with dimorphic alleles and is likely maintained by a chromosomal inversion. In the closely related Papilio memnon; which exhibits a similar mimicry polymorphism; we performed whole-genome sequence analyses in 11 butterflies; which revealed a nearly identical dsx-HDR containing three genes (dsx; Nach-like; and UXT) with dimorphic sequences strictly associated with the mimetic/nonmimetic phenotypes. In addition; expression of these genes; except that of Nach-like in female hind wings; showed differences correlated with phenotype. The dimorphic dsx-HDR in P. memnon is maintained without a chromosomal inversion; suggesting that a separate mechanism causes and maintains allelic divergence in these genes. More abundant accumulation of transposable elements and repetitive sequences in the dsx-HDR than in other genomic regions may contribute to the suppression of chromosomal recombination. Gene trees for Dsx; Nach-like; and UXT indicated that mimetic alleles evolved independently in the two Papilio species. These results suggest that the genomic region involving the above three genes has repeatedly diverged so that two allelic sequences of this region function as developmental switches for mimicry polymorphism in the two Papilio species. The supergene structures revealed here suggest that independent evolutionary processes with different genetic mechanisms have led to parallel evolution of similar female-limited polymorphisms underlying Batesian mimicry in Papilio butterflies.	In 1981 recurrent local bursts of mutability of the yellow gene were observed in a natural population of Drosophila melanogaster from Uman' (Ukraine). A series of y2-like mutations in the yellow gene were recovered during the period 1982 to 1991. Most of the mutants display the y2-phenotype; i.e. mutant yellow color of wings and body cuticle. Ninety-nine y2 mutants were shown to be generated by an inversion that occurred between two hobo elements; one located 129 bp from the start site of yellow transcription; and the other in the distal telomere region. The y2 phenotype was caused by the separation of the body and wing enhancers from the transcription unit. Many of the y2-like alleles were highly unstable and reverted to y+; which again; gave rise to y2-like mutants. We found that the y2-->y+-->y2 transitions were generated by repeated inversions between the two hobo elements mentioned. The y2 and y+ alleles lost their instability after deletion of the hobo element present at the tip of the X chromosome.	Whales in the suborder Mysticeti are filter feeders that use baleen to sift zooplankton and small fish from ocean waters. Adult mysticetes lack teeth; although tooth buds are present in foetal stages. Cladistic analyses suggest that functional teeth were lost in the common ancestor of crown-group Mysticeti. DNA sequences for the tooth-specific genes; ameloblastin (AMBN); enamelin (ENAM) and amelogenin (AMEL); have frameshift mutations and/or stop codons in this taxon; but none of these molecular cavities are shared by all extant mysticetes. Here; we provide the first evidence for pseudogenization of a tooth gene; enamelysin (MMP20); in the common ancestor of living baleen whales. Specifically; pseudogenization resulted from the insertion of a CHR-2 SINE retroposon in exon 2 of MMP20. Genomic and palaeontological data now provide congruent support for the loss of enamel-capped teeth on the common ancestral branch of crown-group mysticetes. The new data for MMP20 also document a polymorphic stop codon in exon 2 of the pygmy sperm whale (Kogia breviceps); which has enamel-less teeth. These results; in conjunction with the evidence for pseudogenization of MMP20 in Hoffmann's two-toed sloth (Choloepus hoffmanni); another enamel-less species; support the hypothesis that the only unique; non-overlapping function of the MMP20 gene is in enamel formation.	The duck-billed platypus (Ornithorhynchus anatinus) belongs to the mammalian subclass Prototheria; which diverged from the Theria line early in mammalian evolution. The platypus genome sequence provides a unique opportunity to illuminate some aspects of the biology and evolution of these animals. We show that several genes implicated in food digestion in the stomach have been deleted or inactivated in platypus. Comparison with other vertebrate genomes revealed that the main genes implicated in the formation and activity of gastric juice have been lost in platypus. These include the aspartyl proteases pepsinogen A and pepsinogens B/C; the hydrochloric acid secretion stimulatory hormone gastrin; and the alpha subunit of the gastric H+/K+-ATPase. Other genes implicated in gastric functions; such as the beta subunit of the H+/K+-ATPase and the aspartyl protease cathepsin E; have been inactivated because of the acquisition of loss-of-function mutations. All of these genes are highly conserved in vertebrates; reflecting a unique pattern of evolution in the platypus genome not previously seen in other mammalian genomes. The observed loss of genes involved in gastric functions might be responsible for the anatomical and physiological differences in gastrointestinal tract between monotremes and other vertebrates; including small size; lack of glands; and high pH of the monotreme stomach. This study contributes to a better understanding of the mechanisms that underlie the evolution of the platypus genome; might extend the less-is-more evolutionary model to monotremes; and provides novel insights into the importance of gene loss events during mammalian evolution. &2 The duck-billed platypus (Ornithorhynchus anatinus) belongs to the mammalian subclass Prototheria; which diverged from the Theria line early in mammalian evolution. The platypus genome sequence provides a unique opportunity to illuminate some aspects of the biology and evolution of these animals. We show that several genes implicated in food digestion in the stomach have been deleted or inactivated in platypus. Comparison with other vertebrate genomes revealed that the main genes implicated in the formation and activity of gastric juice have been lost in platypus. These include the aspartyl proteases pepsinogen A and pepsinogens B/C; the hydrochloric acid secretion stimulatory hormone gastrin; and the alpha subunit of the gastric H+/K+-ATPase. Other genes implicated in gastric functions; such as the beta subunit of the H+/K+-ATPase and the aspartyl protease cathepsin E; have been inactivated because of the acquisition of loss-of-function mutations. All of these genes are highly conserved in vertebrates; reflecting a unique pattern of evolution in the platypus genome not previously seen in other mammalian genomes. The observed loss of genes involved in gastric functions might be responsible for the anatomical and physiological differences in gastrointestinal tract between monotremes and other vertebrates; including small size; lack of glands; and high pH of the monotreme stomach. This study contributes to a better understanding of the mechanisms that underlie the evolution of the platypus genome; might extend the less-is-more evolutionary model to monotremes; and provides novel insights into the importance of gene loss events during mammalian evolution.	The amylase gene (AMY); which codes for a starch-digesting enzyme in animals; underwent several gene copy number gains in humans (Perry et al.; 2007); dogs (Axelsson et al.; 2013); and mice (Schibler et al.; 1982); possibly along with increased starch consumption during the evolution of these species. Here; we present comprehensive evidence for AMY copy number expansions that independently occurred in several mammalian species which consume diets rich in starch. We also provide correlative evidence that AMY gene duplications may be an essential first step for amylase to be expressed in saliva. Our findings underscore the overall importance of gene copy number amplification as a flexible and fast evolutionary mechanism that can independently occur in different branches of the phylogeny. © 2019; Pajic et al.	The amylase gene (AMY); which codes for a starch-digesting enzyme in animals; underwent several gene copy number gains in humans (Perry et al.; 2007); dogs (Axelsson et al.; 2013); and mice (Schibler et al.; 1982); possibly along with increased starch consumption during the evolution of these species. Here; we present comprehensive evidence for AMY copy number expansions that independently occurred in several mammalian species which consume diets rich in starch. We also provide correlative evidence that AMY gene duplications may be an essential first step for amylase to be expressed in saliva. Our findings underscore the overall importance of gene copy number amplification as a flexible and fast evolutionary mechanism that can independently occur in different branches of the phylogeny. © 2019; Pajic et al.	The amylase gene (AMY); which codes for a starch-digesting enzyme in animals; underwent several gene copy number gains in humans (Perry et al.; 2007); dogs (Axelsson et al.; 2013); and mice (Schibler et al.; 1982); possibly along with increased starch consumption during the evolution of these species. Here; we present comprehensive evidence for AMY copy number expansions that independently occurred in several mammalian species which consume diets rich in starch. We also provide correlative evidence that AMY gene duplications may be an essential first step for amylase to be expressed in saliva. Our findings underscore the overall importance of gene copy number amplification as a flexible and fast evolutionary mechanism that can independently occur in different branches of the phylogeny. © 2019; Pajic et al.	The amylase gene (AMY); which codes for a starch-digesting enzyme in animals; underwent several gene copy number gains in humans (Perry et al.; 2007); dogs (Axelsson et al.; 2013); and mice (Schibler et al.; 1982); possibly along with increased starch consumption during the evolution of these species. Here; we present comprehensive evidence for AMY copy number expansions that independently occurred in several mammalian species which consume diets rich in starch. We also provide correlative evidence that AMY gene duplications may be an essential first step for amylase to be expressed in saliva. Our findings underscore the overall importance of gene copy number amplification as a flexible and fast evolutionary mechanism that can independently occur in different branches of the phylogeny. © 2019; Pajic et al.	Benzimidazoles (BZ) are essential components of the limited chemotherapeutic arsenal available to control the global burden of parasitic nematodes. The emerging threat of BZ resistance among multiple nematode species necessitates the development of novel strategies to identify genetic and molecular mechanisms underlying this resistance. All detection of parasitic helminth resistance to BZ is focused on the genotyping of three variant sites in the orthologs of the β-tubulin gene found to confer resistance in the free-living nematode Caenorhabditis elegans. Because of the limitations of laboratory and field experiments in parasitic nematodes; it is difficult to look beyond these three sites to identify additional mechanisms that might contribute to BZ resistance in the field. Here; we took an unbiased genome-wide mapping approach in the free-living nematode species C. elegans to identify the genetic underpinnings of natural resistance to the commonly used BZ; albendazole (ABZ). We found a wide range of natural variation in ABZ resistance in natural C. elegans populations. In agreement with known mechanisms of BZ resistance in parasites; we found that a majority of the variation in ABZ resistance among wild C. elegans strains is caused by variation in the β-tubulin gene ben-1. This result shows empirically that resistance to ABZ naturally exists and segregates within the C. elegans population; suggesting that selection in natural niches could enrich for resistant alleles. We identified 25 distinct ben-1 alleles that are segregating at low frequencies within the C. elegans population; including many novel molecular variants. Population genetic analyses indicate that ben-1 variation arose multiple times during the evolutionary history of C. elegans and provide evidence that these alleles likely occurred recently because of local selective pressures. Additionally; we find purifying selection at all five β-tubulin genes; despite predicted loss-of-function variants in ben-1; indicating that BZ resistance in natural niches is a stronger selective pressure than loss of one β-tubulin gene. Furthermore; we used genome-editing to show that the most common parasitic nematode β-tubulin allele that confers BZ resistance; F200Y; confers resistance in C. elegans. Importantly; we identified a novel genomic region that is correlated with ABZ resistance in the C. elegans population but independent of ben-1 and the other β-tubulin loci; suggesting that there are multiple mechanisms underlying BZ resistance. Taken together; our results establish a population-level resource of nematode natural diversity as an important model for the study of mechanisms that give rise to BZ resistance.	A recent genomewide screen identified 13 transposable elements that are likely to have been adaptive during or after the spread of Drosophila melanogaster out of Africa. One of these insertions; Bari-Juvenile hormone epoxy hydrolase (Bari-Jheh); was associated with the selective sweep of its flanking neutral variation and with reduction of expression of one of its neighboring genes: Jheh3. Here; we provide further evidence that Bari-Jheh insertion is adaptive. We delimit the extent of the selective sweep and show that Bari-Jheh is the only mutation linked to the sweep. Bari-Jheh also lowers the expression of its other flanking gene; Jheh2. Subtle consequences of Bari-Jheh insertion on life-history traits are consistent with the effects of reduced expression of the Jheh genes. Finally; we analyze molecular evolution of Jheh genes in both the long- and the short-term and conclude that Bari-Jheh appears to be a very rare adaptive event in the history of these genes. We discuss the implications of these findings for the detection and understanding of adaptation.	A tomato phytoene synthase gene; Psy1; has recently been isolated as the clone GTOM5 and shown by sequence identity to be the gene from which the major fruit-ripening cDNA clone TOM5 was derived. Sequence analysis of transcripts from two allelic yellow-fruited tomato mutants; mapped to chromosome 3; has shown the lack of carotenoids in fruit of these mutants to be due to the production of aberrant TOM5 transcripts which are unlikely to encode a functional phytoene synthase enzyme. In one mutant (yellow flesh) the aberrant transcript contained a sequence that; by its strong hybridization to a wide size range of genomic fragments; appeared to be repeated many times within the genome. Southern and PCR analysis of the phytoene synthase genes in the mutant revealed restriction fragment length polymorphisms; suggesting that the production of altered mRNAs was associated with specific genomic rearrangements. Constitutive over-expression of a TOM5 cDNA clone in transgenic mutant plants restored synthesis of the carotenoid lycopene in ripening fruit and also led to unscheduled pigment production in other cell types. In some mutant plants transformed with the TOM5 cDNA construct; inhibition of carotenoid production in immature green fruit; leaves and flowers was observed; due to the phenomenon of co-suppression; indicating that different insertion events with the same gene construct can lead to overexpression or co-suppression in transgenic plants. Green organs of these plants were susceptible to photobleaching; due to the lack of carotenoids. These results suggest the existence of separate Psy genes for carotenoid synthesis in green organs.	Fungal plant pathogens pose major threats to crop yield and sustainable food production if they are highly adapted to their host and the local environment. Variation in gene expression contributes to phenotypic diversity within fungal species and affects adaptation. However; very few cases of adaptive regulatory changes have been reported in fungi and the underlying mechanisms remain largely unexplored. Fungal pathogen genomes are highly plastic and harbor numerous insertions of transposable elements; which can potentially contribute to gene expression regulation. In this work; we elucidated how transposable elements contribute to variation in melanin accumulation; a quantitative trait in fungi that affects survival under stressful conditions. We demonstrated that differential transcriptional regulation of the gene encoding the transcription factor Zmr1; which controls expression of the genes in the melanin biosynthetic gene cluster; is responsible for variation in melanin accumulation in the fungal plant pathogen Zymoseptoria tritici. We show that differences in melanin levels between two strains of Z. tritici are due to two levels of transcriptional regulation: (1) variation in the promoter sequence of Zmr1 and (2) an insertion of transposable elements upstream of the Zmr1 promoter. Remarkably; independent insertions of transposable elements upstream of Zmr1 occurred in 9% of Z. tritici strains from around the world and negatively regulated Zmr1 expression; contributing to variation in melanin accumulation. Our studies identified two levels of transcriptional control that regulate the synthesis of melanin. We propose that these regulatory mechanisms evolved to balance the fitness costs associated with melanin production against its positive contribution to survival in stressful environments. &2 Fungal plant pathogens pose major threats to crop yield and sustainable food production if they are highly adapted to their host and the local environment. Variation in gene expression contributes to phenotypic diversity within fungal species and affects adaptation. However; very few cases of adaptive regulatory changes have been reported in fungi and the underlying mechanisms remain largely unexplored. Fungal pathogen genomes are highly plastic and harbor numerous insertions of transposable elements; which can potentially contribute to gene expression regulation. In this work; we elucidated how transposable elements contribute to variation in melanin accumulation; a quantitative trait in fungi that affects survival under stressful conditions. We demonstrated that differential transcriptional regulation of the gene encoding the transcription factor Zmr1; which controls expression of the genes in the melanin biosynthetic gene cluster; is responsible for variation in melanin accumulation in the fungal plant pathogen Zymoseptoria tritici. We show that differences in melanin levels between two strains of Z. tritici are due to two levels of transcriptional regulation: (1) variation in the promoter sequence of Zmr1 and (2) an insertion of transposable elements upstream of the Zmr1 promoter. Remarkably; independent insertions of transposable elements upstream of Zmr1 occurred in 9% of Z. tritici strains from around the world and negatively regulated Zmr1 expression; contributing to variation in melanin accumulation. Our studies identified two levels of transcriptional control that regulate the synthesis of melanin. We propose that these regulatory mechanisms evolved to balance the fitness costs associated with melanin production against its positive contribution to survival in stressful environments.	The corn snake (Pantherophis guttatus) is a new model species particularly appropriate for investigating the processes generating colours in reptiles because numerous colour and pattern mutants have been isolated in the last five decades. Using our captive-bred colony of corn snakes; transcriptomic and genomic next-generation sequencing; exome assembly; and genotyping of SNPs in multiple families; we delimit the genomic interval bearing the causal mutation of amelanism; the oldest colour variant observed in that species. Proceeding with sequencing the candidate gene OCA2 in the uncovered genomic interval; we identify that the insertion of an LTR-retrotransposon in its 11(th) intron results in a considerable truncation of the p protein and likely constitutes the causal mutation of amelanism in corn snakes. As amelanistic snakes exhibit white; instead of black; borders around an otherwise normal pattern of dorsal orange saddles and lateral blotches; our results indicate that melanocytes lacking melanin are able to participate to the normal patterning of other colours in the skin. In combination with research in the zebrafish; this work opens the perspective of using corn snake colour and pattern variants to investigate the generative processes of skin colour patterning shared among major vertebrate lineages.	The mutable flaked (or af) lines of the common morning glory bear white flowers with colored flakes and sectors. The af allele shows incomplete dominance. Plants in the heterozygous state A/af bear lightly colored flowers with intensely colored flakes and occasionally with white sectors. We showed that the mutable af allele is caused by insertion of a new transposable element; Tip100; into the CHS-D gene intron. Tip100 is 3.9 kb long and belongs to the Ac/Ds family. Although the timing and frequency of the flower variegation vary in different lines; they carry an identical mutable allele. We also noticed that a flaked subline; bearing variegated flowers; carries a Tip100 derivative; Tip100-1. The structure of Tip100-1 contains an additional 48 bp terminal sequence as tandem repeats and its integration site is identical to that of Tip100. Another line; with stable white flowers; is a double mutant carrying two copies of Tip100 in the CHS-D gene. These results are discussed with regard to the variegated phenotypes of flowers in various mutable lines.	The mutable flaked (or af) lines of the common morning glory bear white flowers with colored flakes and sectors. The af allele shows incomplete dominance. Plants in the heterozygous state A/af bear lightly colored flowers with intensely colored flakes and occasionally with white sectors. We showed that the mutable af allele is caused by insertion of a new transposable element; Tip100; into the CHS-D gene intron. Tip100 is 3.9 kb long and belongs to the Ac/Ds family. Although the timing and frequency of the flower variegation vary in different lines; they carry an identical mutable allele. We also noticed that a flaked subline; bearing variegated flowers; carries a Tip100 derivative; Tip100-1. The structure of Tip100-1 contains an additional 48 bp terminal sequence as tandem repeats and its integration site is identical to that of Tip100. Another line; with stable white flowers; is a double mutant carrying two copies of Tip100 in the CHS-D gene. These results are discussed with regard to the variegated phenotypes of flowers in various mutable lines.	Mutations that add; subtract; rearrange; or otherwise refashion genome structure often affect phenotypes; although the fragmented nature of most contemporary assemblies obscures them. To discover such mutations; we assembled the first new reference-quality genome of Drosophila melanogaster since its initial sequencing. By comparing this new genome to the existing D. melanogaster assembly; we created a structural variant map of unprecedented resolution and identified extensive genetic variation that has remained hidden until now. Many of these variants constitute candidates underlying phenotypic variation; including tandem duplications and a transposable element insertion that amplifies the expression of detoxification-related genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high-quality reference genomes are to deciphering phenotypes.	The increase in availability of whole genome sequences makes it possible to search for evidence of adaptation at an unprecedented scale. Despite recent progress; our understanding of the adaptive process is still very limited due to the difficulties in linking adaptive mutations to their phenotypic effects. In this study; we integrated different levels of biological information to pinpoint the ecologically relevant fitness effects and the underlying molecular and biochemical mechanisms of a putatively adaptive TE insertion in Drosophila melanogaster: the pogo transposon FBti0019627. We showed that other than being incorporated into Kmn1 transcript; FBti0019627 insertion also affects the polyadenylation signal choice of CG11699 gene. Consequently; only the short 3'UTR transcript of CG11699 gene is produced and the expression level of this gene is higher in flies with the insertion. Our results indicated that increased CG11699 expression leads to xenobiotic stress resistance through increased ALDH-III activity: flies with FBti0019627 insertion showed increased survival rate in response to benzaldehyde; a natural xenobiotic; and to carbofuran; a synthetic insecticide. Although differences in survival rate between flies with and without the insertion were not always significant; when they were; they were consistent with FBti0019627 mediating resistance to xenobiotics. Taken together; our results provide a plausible explanation for the increase in frequency of FBti0019627 in natural populations of D. melanogaster and add to the limited number of examples in which a natural genetic mutation has been linked to its ecologically relevant phenotype. Furthermore; the widespread distribution of TEs across the tree of life and conservation of stress response pathways across organisms make our results relevant not only for Drosophila; but for other organisms as well.	Darwin's studies on heterostyly in Primula described two floral morphs; pin and thrum; with reciprocal anther and stigma heights that promote insect-mediated cross-pollination. This key innovation evolved independently in several angiosperm families. Subsequent studies on heterostyly in Primula contributed to the foundation of modern genetic theory and the neo-Darwinian synthesis. The established genetic model for Primula heterostyly involves a diallelic S locus comprising several genes; with rare recombination events that result in self-fertile homostyle flowers with anthers and stigma at the same height. Here we reveal the S locus supergene as a tightly linked cluster of thrum-specific genes that are absent in pins. We show that thrums are hemizygous not heterozygous for the S locus; which suggests that homostyles do not arise by recombination between S locus haplotypes as previously proposed. Duplication of a floral homeotic gene 51.7 million years (Myr) ago; followed by its neofunctionalization; created the current S locus assemblage which led to floral heteromorphy in Primula. Our findings provide new insights into the structure; function and evolution of this archetypal supergene.	Convergent evolution provides a rare; natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning; population genomic resequencing; association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene; WntA; are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore; characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together; our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time.	The naturally occurring waxy and low-amylose variants of foxtail millet and other cereals; like rice and barley; originated in East and Southeast Asia under human selection for sticky foods. Mutations in the GBSS1 gene for granule-bound starch synthase 1 are known to be associated with these traits. We have analyzed the gene in foxtail millet; and found that; in this species; these traits were originated by multiple independent insertions of transposable elements and by subsequent secondary insertions into these elements or deletion of parts of the elements. The structural analysis of transposable elements inserted in the GBSS1 gene revealed that the non-waxy was converted to the low-amylose phenotype once; while shifts from non-waxy to waxy occurred three times; from low amylose to waxy once and from waxy to low amylose once. The present results; and the geographical distribution of different waxy molecular types; strongly suggest that these types originated independently and were dispersed into their current distribution areas. The patterns of GBSS1 variation revealed here suggest that foxtail millet may serve as a key to solving the mystery of the origin of waxy-type cereals in Asia. The GBSS1 gene in foxtail millet provides a new example of the evolution of a gene involved in the processes of domestication and its post-domestication fate under the influence of human selection.	The naturally occurring waxy and low-amylose variants of foxtail millet and other cereals; like rice and barley; originated in East and Southeast Asia under human selection for sticky foods. Mutations in the GBSS1 gene for granule-bound starch synthase 1 are known to be associated with these traits. We have analyzed the gene in foxtail millet; and found that; in this species; these traits were originated by multiple independent insertions of transposable elements and by subsequent secondary insertions into these elements or deletion of parts of the elements. The structural analysis of transposable elements inserted in the GBSS1 gene revealed that the non-waxy was converted to the low-amylose phenotype once; while shifts from non-waxy to waxy occurred three times; from low amylose to waxy once and from waxy to low amylose once. The present results; and the geographical distribution of different waxy molecular types; strongly suggest that these types originated independently and were dispersed into their current distribution areas. The patterns of GBSS1 variation revealed here suggest that foxtail millet may serve as a key to solving the mystery of the origin of waxy-type cereals in Asia. The GBSS1 gene in foxtail millet provides a new example of the evolution of a gene involved in the processes of domestication and its post-domestication fate under the influence of human selection.	The naturally occurring waxy and low-amylose variants of foxtail millet and other cereals; like rice and barley; originated in East and Southeast Asia under human selection for sticky foods. Mutations in the GBSS1 gene for granule-bound starch synthase 1 are known to be associated with these traits. We have analyzed the gene in foxtail millet; and found that; in this species; these traits were originated by multiple independent insertions of transposable elements and by subsequent secondary insertions into these elements or deletion of parts of the elements. The structural analysis of transposable elements inserted in the GBSS1 gene revealed that the non-waxy was converted to the low-amylose phenotype once; while shifts from non-waxy to waxy occurred three times; from low amylose to waxy once and from waxy to low amylose once. The present results; and the geographical distribution of different waxy molecular types; strongly suggest that these types originated independently and were dispersed into their current distribution areas. The patterns of GBSS1 variation revealed here suggest that foxtail millet may serve as a key to solving the mystery of the origin of waxy-type cereals in Asia. The GBSS1 gene in foxtail millet provides a new example of the evolution of a gene involved in the processes of domestication and its post-domestication fate under the influence of human selection.	The naturally occurring waxy and low-amylose variants of foxtail millet and other cereals; like rice and barley; originated in East and Southeast Asia under human selection for sticky foods. Mutations in the GBSS1 gene for granule-bound starch synthase 1 are known to be associated with these traits. We have analyzed the gene in foxtail millet; and found that; in this species; these traits were originated by multiple independent insertions of transposable elements and by subsequent secondary insertions into these elements or deletion of parts of the elements. The structural analysis of transposable elements inserted in the GBSS1 gene revealed that the non-waxy was converted to the low-amylose phenotype once; while shifts from non-waxy to waxy occurred three times; from low amylose to waxy once and from waxy to low amylose once. The present results; and the geographical distribution of different waxy molecular types; strongly suggest that these types originated independently and were dispersed into their current distribution areas. The patterns of GBSS1 variation revealed here suggest that foxtail millet may serve as a key to solving the mystery of the origin of waxy-type cereals in Asia. The GBSS1 gene in foxtail millet provides a new example of the evolution of a gene involved in the processes of domestication and its post-domestication fate under the influence of human selection.	The naturally occurring waxy and low-amylose variants of foxtail millet and other cereals; like rice and barley; originated in East and Southeast Asia under human selection for sticky foods. Mutations in the GBSS1 gene for granule-bound starch synthase 1 are known to be associated with these traits. We have analyzed the gene in foxtail millet; and found that; in this species; these traits were originated by multiple independent insertions of transposable elements and by subsequent secondary insertions into these elements or deletion of parts of the elements. The structural analysis of transposable elements inserted in the GBSS1 gene revealed that the non-waxy was converted to the low-amylose phenotype once; while shifts from non-waxy to waxy occurred three times; from low amylose to waxy once and from waxy to low amylose once. The present results; and the geographical distribution of different waxy molecular types; strongly suggest that these types originated independently and were dispersed into their current distribution areas. The patterns of GBSS1 variation revealed here suggest that foxtail millet may serve as a key to solving the mystery of the origin of waxy-type cereals in Asia. The GBSS1 gene in foxtail millet provides a new example of the evolution of a gene involved in the processes of domestication and its post-domestication fate under the influence of human selection.	The naturally occurring waxy and low-amylose variants of foxtail millet and other cereals; like rice and barley; originated in East and Southeast Asia under human selection for sticky foods. Mutations in the GBSS1 gene for granule-bound starch synthase 1 are known to be associated with these traits. We have analyzed the gene in foxtail millet; and found that; in this species; these traits were originated by multiple independent insertions of transposable elements and by subsequent secondary insertions into these elements or deletion of parts of the elements. The structural analysis of transposable elements inserted in the GBSS1 gene revealed that the non-waxy was converted to the low-amylose phenotype once; while shifts from non-waxy to waxy occurred three times; from low amylose to waxy once and from waxy to low amylose once. The present results; and the geographical distribution of different waxy molecular types; strongly suggest that these types originated independently and were dispersed into their current distribution areas. The patterns of GBSS1 variation revealed here suggest that foxtail millet may serve as a key to solving the mystery of the origin of waxy-type cereals in Asia. The GBSS1 gene in foxtail millet provides a new example of the evolution of a gene involved in the processes of domestication and its post-domestication fate under the influence of human selection.		The combination of QTL mapping studies of synthetic lines and association mapping studies of natural diversity represents an opportunity to throw light on the genetically based variation of quantitative traits. With the positional information provided through quantitative trait locus (QTL) mapping; which often leads to wide intervals encompassing numerous genes; it is now feasible to directly target candidate genes that are likely to be responsible for the observed variation in completely sequenced genomes and to test their effects through association genetics. This approach was performed in grape; a newly sequenced genome; to decipher the genetic architecture of anthocyanin content. Grapes may be either white or colored; ranging from the lightest pink to the darkest purple tones according to the amount of anthocyanin accumulated in the berry skin; which is a crucial trait for both wine quality and human nutrition. Although the determinism of the white phenotype has been fully identified; the genetic bases of the quantitative variation of anthocyanin content in berry skin remain unclear. A single QTL responsible for up to 62% of the variation in the anthocyanin content was mapped on a Syrah x Grenache F(1) pseudo-testcross. Among the 68 unigenes identified in the grape genome within the QTL interval; a cluster of four Myb-type genes was selected on the basis of physiological evidence (VvMybA1; VvMybA2; VvMybA3; and VvMybA4). From a core collection of natural resources (141 individuals); 32 polymorphisms revealed significant association; and extended linkage disequilibrium was observed. Using a multivariate regression method; we demonstrated that five polymorphisms in VvMybA genes except VvMybA4 (one retrotransposon; three single nucleotide polymorphisms and one 2-bp insertion/deletion) accounted for 84% of the observed variation. All these polymorphisms led to either structural changes in the MYB proteins or differences in the VvMybAs promoters. We concluded that the continuous variation in anthocyanin content in grape was explained mainly by a single gene cluster of three VvMybA genes. The use of natural diversity helped to reduce one QTL to a set of five quantitative trait nucleotides and gave a clear picture of how isogenes combined their effects to shape grape color. Such analysis also illustrates how isogenes combine their effect to shape a complex quantitative trait and enables the definition of markers directly targeted for upcoming breeding programs.		The number of vertebrae in pigs varies and is associated with body size. Wild boars have 19 vertebrae; but European commercial breeds for pork production have 20 to 23 vertebrae. We previously identified two quantitative trait loci (QTLs) for number of vertebrae on Sus scrofa chromosomes (SSC) 1 and 7; and reported that an orphan nuclear receptor; NR6A1; was located at the QTL on SSC1. At the NR6A1 locus; wild boars and Asian local breed pigs had the wild-type allele and European commercial-breed pigs had an allele associated with increased numbers of vertebrae (number-increase allele). Here; we performed a map-based study to define the other QTL; on SSC7; for which we detected genetic diversity in European commercial breeds. Haplotype analysis with microsatellite markers revealed a 41-kb conserved region within all the number-increase alleles in the present study. We also developed single nucleotide polymorphisms (SNPs) in the 450-kb region around the QTL and used them for a linkage disequilibrium analysis and an association study in 199 independent animals. Three haplotype blocks were detected; and SNPs in the 41-kb region presented the highest associations with the number of vertebrae. This region encodes an uncharacterized hypothetical protein that is not a member of any other known gene family. Orthologs appear to exist not only in mammals but also birds and fish. This gene; which we have named vertnin (VRTN) is a candidate for the gene associated with variation in vertebral number. In pigs; the number-increase allele was expressed more abundantly than the wild-type allele in embryos. Among candidate polymorphisms; there is an insertion of a SINE element (PRE1) into the intron of the Q allele as well as the SNPs in the promoter region. Genetic diversity of VRTN is the suspected cause of the heterogeneity of the number of vertebrae in commercial-breed pigs; so the polymorphism information should be directly useful for assessing the genetic ability of individual animals. The number-increase allele of swine VRTN was suggested to add an additional thoracic segment to the animal. Functional analysis of VRTN may provide novel findings in the areas of developmental biology.		In Old World primates; TRIM5-alpha confers a potent block to human immunodeficiency virus type 1 (HIV-1) infection that acts after virus entry into cells. Cyclophilin A (CypA) binding to viral capsid protects HIV-1 from a similar activity in human cells. Among New World primates; only owl monkeys exhibit post-entry restriction of HIV-1 (ref. 1). Paradoxically; the barrier to HIV-1 in owl monkey cells is released by capsid mutants or drugs that disrupt capsid interaction with CypA. Here we show that knockdown of owl monkey CypA by RNA interference (RNAi) correlates with suppression of anti-HIV-1 activity. However; reintroduction of CypA protein to RNAi-treated cells did not restore antiviral activity. A search for additional RNAi targets unearthed TRIMCyp; an RNAi-responsive messenger RNA encoding a TRIM5-CypA fusion protein. TRIMCyp accounts for post-entry restriction of HIV-1 in owl monkeys and blocks HIV-1 infection when transferred to otherwise infectable human or rat cells. It seems that TRIMCyp arose after the divergence of New and Old World primates when a LINE-1 retrotransposon catalysed the insertion of a CypA complementary DNA into the TRIM5 locus. This is the first vertebrate example of a chimaeric gene generated by this mechanism of exon shuffling.	Edible fruits; such as that of the tomato plant and other vegetable crops; are markedly diverse in shape and size. SUN; one of the major genes controlling the elongated fruit shape of tomato; was positionally cloned and found to encode a member of the IQ67 domain-containing family. We show that the locus arose as a result of an unusual 24.7-kilobase gene duplication event mediated by the long terminal repeat retrotransposon Rider. This event resulted in a new genomic context that increased SUN expression relative to that of the ancestral copy; culminating in an elongated fruit shape. Our discovery demonstrates that retrotransposons may be a major driving force in genome evolution and gene duplication; resulting in phenotypic change in plants.	Activity of the enzyme ADPglucose pyrophosphorylase is known to be reduced in maize (Zea mays L.) endosperm mutants at two independent loci; Shrunken-2 (Sh(2)) and Brittle-2 (Bt(2)). Spinach leaf ADPglucose pyrophosphorylase has previously been shown to comprise two subunits of 51 and 54 kilodaltons. Anti-bodies raised to each of the two subunits of spinach leaf ADPglucose pyrophosphorylase were found to cross-react to different bands on Western blots prepared from polyacrylamide gel electrophoresis separated wild-type maize endosperm proteins. The anti-spinach leaf 51 kilodalton subunit antibody cross-reacted with a 55 kilodalton maize endosperm protein and the anti-spinach leaf 54 kilodalton subunit antibody cross-reacted with a 60 kilodalton maize endosperm protein. These immunological reactions were observed in maize endosperm extracts and with a highly purified preparation of maize endosperm ADPglucose pyrophosphorylase. Mutant bt(2) endosperm lacked the 55 kilodalton subunit while mutant sh(2) endosperm lacked the 60 kilodalton subunit on Western blots. These results suggest that the maize endosperm ADPglucose pyrophosphorylase is made up of two immunologically dissimilar subunits and that the bt(2) and sh(2) mutations cause reduction in ADPglucose pyrophosphorylase activity through the lack of one of these two subunits. An ADPglucose pyrophosphorylase cDNA clone antigenically selected from a rice seed cDNA expression library was found to hybridize strongly with a cDNA corresponding to a maize endosperm transcript which is absent in a W64A bt(2) mutant. Thus; the bt(2) mutant causes the absence not only of the small subunit but of the corresponding transcript. Bt(2) is implicated as the structural gene for the small (54 kilodalton) subunit of maize endosperm ADPglucose pyrophosphorylase.	Traditionally; Sicilian blood oranges (Citrus sinensis) have been associated with cardiovascular health; and consumption has been shown to prevent obesity in mice fed a high-fat diet. Despite increasing consumer interest in these health-promoting attributes; production of blood oranges remains unreliable due largely to a dependency on cold for full color formation. We show that Sicilian blood orange arose by insertion of a Copia-like retrotransposon adjacent to a gene encoding Ruby; a MYB transcriptional activator of anthocyanin production. The retrotransposon controls Ruby expression; and cold dependency reflects the induction of the retroelement by stress. A blood orange of Chinese origin results from an independent insertion of a similar retrotransposon; and color formation in its fruit is also cold dependent. Our results suggest that transposition and recombination of retroelements are likely important sources of variation in Citrus.	Traditionally; Sicilian blood oranges (Citrus sinensis) have been associated with cardiovascular health; and consumption has been shown to prevent obesity in mice fed a high-fat diet. Despite increasing consumer interest in these health-promoting attributes; production of blood oranges remains unreliable due largely to a dependency on cold for full color formation. We show that Sicilian blood orange arose by insertion of a Copia-like retrotransposon adjacent to a gene encoding Ruby; a MYB transcriptional activator of anthocyanin production. The retrotransposon controls Ruby expression; and cold dependency reflects the induction of the retroelement by stress. A blood orange of Chinese origin results from an independent insertion of a similar retrotransposon; and color formation in its fruit is also cold dependent. Our results suggest that transposition and recombination of retroelements are likely important sources of variation in Citrus.	The RPS5 and RFL1 disease resistance genes of Arabidopsis ecotype Col-0 are oriented in tandem and are separated by 1.4 kb. The Ler-0 ecotype contains RFL1; but lacks RPS5. Sequence analysis of the RPS5 deletion region in Ler-0 revealed the presence of an Ac-like transposable element; which we have designated Tag2. Southern hybridization analysis of six Arabidopsis ecotypes revealed 4-11 Tag2-homologous sequences in each; indicating that this element is ubiquitous in Arabidopsis and has been active in recent evolutionary time. The Tag2 insertion adjacent to RFL1 was unique to the Ler-0 ecotype; however; and was not present in two other ecotypes that lack RPS5. DNA sequence from the latter ecotypes lacked a transposon footprint; suggesting that insertion of Tag2 occurred after the initial deletion of RPS5. The deletion breakpoint contained a 192-bp insertion that displayed hallmarks of a nonhomologous DNA end-joining event. We conclude that loss of RPS5 was caused by a double-strand break and subsequent repair; and cannot be attributed to unequal crossing over between resistance gene homologs.	Understanding which genes contribute to evolutionary change and the nature of the alterations in them are fundamental challenges in evolution. We analyzed regulatory and enzymatic genes in the maize anthocyanin pathway as related to the evolution of anthocyanin-pigmented kernels in maize from colorless kernels of its progenitor; teosinte. Genetic tests indicate that teosinte possesses functional alleles at all enzymatic loci. At two regulatory loci; most teosintes possess alleles that encode functional proteins; but ones that are not expressed during kernel development and not capable of activating anthocyanin biosynthesis there. We investigated nucleotide polymorphism at one of the regulatory loci; cl. Several observations suggest that cl has not evolved in a strictly neutral manner; including an exceptionally low level of polymorphism and a biased representation of haplotypes in maize. Curiously; sequence data show that most of our teosinte samples possess a promoter element necessary for the activation of the anthocyanin pathway during kernel development; although genetic tests indicate that teosinte cl alleles are not active during kernel development. Our analyses suggest that the evolution of the purple kernels resulted from changes in cis regulatory elements at regulatory loci and not changes in either regulatory protein function nor the enzymatic loci.	Transposable elements (TEs) are known to provide DNA for host regulatory functions; but the mechanisms underlying the transformation of TEs into cis-regulatory elements are unclear. In humans two TEs--MER20 and MER39--contribute the enhancer/promoter for decidual prolactin (dPRL); which is dramatically induced during pregnancy. We show that evolution of the strong human dPRL promoter was a multistep process that took millions of years. First; MER39 inserted near MER20 in the primate/rodent ancestor; and then there were two phases of activity enhancement in primates. Through the mapping of causal nucleotide substitutions; we demonstrate that strong promoter activity in apes involves epistasis between transcription factor binding sites (TFBSs) ancestral to MER39 and derived sites. We propose a mode of molecular evolution that describes the process by which MER20/MER39 was transformed into a strong promoter; called "epistatic capture." Epistatic capture is the stabilization of a TFBS that is ancestral but variable in outgroup lineages; and is fixed in the ingroup because of epistatic interactions with derived TFBSs. Finally; we note that evolution of human promoter activity coincides with the emergence of a unique reproductive character in apes; highly invasive placentation. Because prolactin communicates with immune cells during pregnancy; which regulate fetal invasion into maternal tissues; we speculate that ape dPRL promoter activity evolved in response to increased invasiveness of ape fetal tissue.	Genetic analyses suggested that the opaque-2 (o2) locus in maize acts as a positive; transacting; transcriptional activator of the zein seed storage-protein genes. Because isolation of the gene is requisite to understanding the molecular details of this regulation; transposon mutagenesis with the transposable element suppressor-mutator (Spm) was carried out; and three mutable o2 alleles were obtained. One of these alleles contained an 8.3-kilobase autonomous Spm; another a 6.8-kilobase nonautonomous Spm; and the third an unidentified transposon that is unrelated to Spm. A DNA sequence flanking the autonomous Spm insertion was verified to be o2-specific and provided a probe to clone a wild-type allele. Northern blots indicated that the gene is expressed in wild-type endosperm but not in leaf tissues or in endosperms homozygous for a mutant allele of the O2 gene. A transcript was detected in endosperms homozygous for mutations at opaque-7 and floury-2; an indication that O2 expression is independent of these two other putative regulators of zein synthesis.	The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time. Until very recently; however; such studies have been limited by our inability to systematically find mutations in evolved organisms. We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes -- including point mutations; structural changes; and insertion variation -- that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in either glucose; sulfate; or phosphate-limited chemostats for approximately 200 generations. We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation. Global nucleotide variation detection in ten clonal isolates identified 32 point mutations. On the basis of mutation frequencies; we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of the continuous phase in the chemostat. We relate these genotypic changes to phenotypic outcomes; namely global patterns of gene expression; and to increases in fitness by 5-50%. We found that the spectrum of available mutations in glucose- or phosphate-limited environments combined with the batch phase population dynamics early in our experiments allowed several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast; sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes. Thus; the reproducibility of evolution varies with specific selective pressures; reflecting the constraints inherent in the system-level organization of metabolic processes in the cell. We were able to relate some of the observed adaptive mutations (e.g.; transporter gene amplifications) to known features of the relevant metabolic pathways; but many of the mutations pointed to genes not previously associated with the relevant physiology. Thus; in addition to answering basic mechanistic questions about evolutionary mechanisms; our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways.	The L6 rust resistance gene from flax was cloned after tagging with the maize transposable element Activator. The gene is predicted to encode two products of 1294 and 705 amino acids that result from alternatively spliced transcripts. The longer product is similar to the products of two other plant disease resistance genes; the tobacco mosaic virus resistance gene N of tobacco and the bacterial resistance gene RPS2 of Arabidopsis. The similarity involves the presence of a nucleotide (ATP/GTP) binding site and several other amino acid motifs of unknown function in the N-terminal half of the polypeptides and a leucine-rich region in the C-terminal half. The truncated product of L6; which lacks most of the leucine-rich C-terminal region; is similar to the truncated product that is predicted from an alternative transcript of the N gene. The L6; N; and RPS2 genes; which control resistance to three widely different pathogen types; are the foundation of a class of plant disease resistance genes that can be referred to as nucleotide binding site/leucine-rich repeat resistance genes.	The Dominant White locus (W) in the domestic cat demonstrates pleiotropic effects exhibiting complete penetrance for absence of coat pigmentation and incomplete penetrance for deafness and iris hypopigmentation. We performed linkage analysis using a pedigree segregating White to identify KIT (Chr. B1) as the feline W locus. Segregation and sequence analysis of the KIT gene in two pedigrees (P1 and P2) revealed the remarkable retrotransposition and evolution of a feline endogenous retrovirus (FERV1) as responsible for two distinct phenotypes of the W locus; Dominant White; and white spotting. A full-length (7125 bp) FERV1 element is associated with white spotting; whereas a FERV1 long terminal repeat (LTR) is associated with all Dominant White individuals. For purposes of statistical analysis; the alternatives of wild-type sequence; FERV1 element; and LTR-only define a triallelic marker. Taking into account pedigree relationships; deafness is genetically linked and associated with this marker; estimated P values for association are in the range of 0.007 to 0.10. The retrotransposition interrupts a DNAase I hypersensitive site in KIT intron 1 that is highly conserved across mammals and was previously demonstrated to regulate temporal and tissue-specific expression of KIT in murine hematopoietic and melanocytic cells. A large-population genetic survey of cats (n = 270); representing 30 cat breeds; supports our findings and demonstrates statistical significance of the FERV1 LTR and full-length element with Dominant White/blue iris (P < 0.0001) and white spotting (P < 0.0001); respectively. Copyright © 2014 David et al.	The HM1 gene in maize controls both race-specific resistance to the fungus Cochliobolus carbonum race 1 and expression of the NADPH (reduced form of nicotinamide adenine dinucleotide phosphate)-dependent HC toxin reductase (HCTR); which inactivates HC toxin; a cyclic tetrapeptide produced by the fungus to permit infection. Several HM1 alleles were generated and cloned by transposon-induced mutagenesis. The sequence of wild-type HM1 shares homology with dihydroflavonol-4-reductase genes from maize; petunia; and snap-dragon. Sequence homology is greatest in the beta alpha beta-dinucleotide binding fold that is conserved among NADPH- and NADH (reduced form of nicotinamide adenine dinucleotide)-dependent reductases and dehydrogenases. This indicates that HM1 encodes HCTR.	Transgenic cotton expressing Bacillus thuringiensis (Bt) toxins has been widely adopted to control some key lepidopteran pests including the bollworm Helicoverpa armigera. Evolution of resistance to Bt cotton by target pests is a major threat to the continued success of Bt cotton. Previous results revealed 3 null alleles (r1-r3) of a cadherin gene (Ha_BtR) conferring Cry1Ac resistance in H. armigera. An F(1) screen of 123 single-pair families was conducted between a Cry1Ac-resistant strain (the SCD-r1 strain; homozygous for the r1 allele of Ha_BtR) and field-derived insects from Jiangpu population (Jiangsu province; China) in 2008. Five new null alleles of Ha_BtR (r4-r8) were identified in six candidate single-pair families. These null alleles were created through either an insertion or a point mutation. Interestingly; intact alleles of Ha_BtR were found in two field-derived insects from another two candidate single-pair families. It suggests that these two field-derived insects may carry novel resistance alleles of Ha_BtR; with missense mutations resulting in a non-functional cadherin protein; or a major dominant mutation at a locus other than cadherin. The resistance allele frequency of Ha_BtR was detected at an appreciable level (0.024) in the Jiangpu population of H. armigera in 2008. Together with previous findings; a total of eight different resistance alleles of Ha_BtR were identified from three Chinese strains of H. armigera. Mutational diversity of Ha_BtR could impair DNA screening for Bt resistance allele frequency in the field; and an F(1) screen should be used routinely for monitoring cadherin-based resistance allele frequencies in H. armigera. 2010 Elsevier Ltd. All rights reserved.
6	Publication Year	1990	2014	2008	1989	PDF	PDF	PDF				2007				PDF		PDF		PDF	1986		2009																	2019	2019	2009	2019	2019	2019	2016	2012	2019	2013	2004	2003	2003	2003	1999	1995	2001	2018	2000	2011	2008 &2 2008	2019	2019	2019	2019	2018	2009	1993	2018 &2 2018	2015	1998	1998	2018	2014	2016	2014	2005	2005	2005	2005	2005	2005	2004	2009	2004	2011	2008	2004	2008	1990	2012	2012	1999	1996	2012	1987	2008	1995	2014	1992	2010
7	Main PMID	2153053,1	25085922,1	18633349,1	2559311,1	17316172	10611384	17492423	14968307	22984469	17270013	17257169	22286805	11158635	17191344	19629571	14617082	17029561	17029561	8312739	3780665	19947977	19386809	22384375	11244116	16407134	26352475	18593744	30118567	16453519	8180498	14617082	9428004	31323150	31321495	31396563	31371717	31420737	30940818	31637460,1	31422154,1	18808453,1	31481212,1	31467598,1	31468029,1	28439533,1	22386310,1	31257142,1	24260296,1	14745026,1	12519916,1	12519916,1	12519916,1	10333570,1	8618845,1	11550893,1	29675466,1	10778753,1	20861053,1	18482448.1 &2 18482448.1	31084707,1	31084707,1	31084707,1	31084707,1	30372484,1	19458110,1	8343597,1	30012138.1 &2 30012138.1	26597053,1	9881157,1	9881157,1	29255259,1	25122208,1	27909301,1	25198507,1	16133169,1	16133169,1	16133169,1	16133169,1	16133169,1	16133169,1	15143274,1	19720862,1	15143274,1	21232157,1	18299570,1	15243629,1	18339939,1	16667400,1	22427337,1	22427337,1	10101179,1	8807310,1	22733751,1	2823388,1	19079573,1	7549479,1	25085922,1	1359642,1	20079435,1
8	Additional PMID																																														28916771,1										27708422,1			&2						25912044,1	29505963,1	&2				29255259.1;25236448.1															15326303,1		1967077,1			20336072,1	22778424,1						9465077,1	16935222,1
9	Generic Gene Name	SBEI	Kit		P1							DFR-B	OsCHI		Glu-1	GmphyA2		P1 and P2	P1 and P2		wx (waxy)	TFL1	APO1																		ABCA2	Pit	AN2	CYP19A1	rhg1s	Eda	Zic1	e	Cyp6g1	Cyp6g1	Hsp70Ba	Hsp70Ba	Hsp70Ba	Hn	Gpdh	Sod1	dsx	y	MMP20	CTSE	Amy1	Amy1	Amy1	Amy1	TUB2	JHEH	PSY1	CMR1	OCA2	CHSD	CHSD	Cyp28d1	Dmel\CG11699	GLO	WntA	waxy	waxy	waxy	waxy	waxy	waxy	VvmybA1	VvmybA1	VvmybA1	Vrtn	TRIM5	TRIM5	100147716	SH2	Ruby	Ruby	RPS5	Z138B04_Z333J11.11	PRL	O2	CUP1-1	L6	Kit	hm1	ABCA2
10	UniProtKB_ID	Q41058	P05532		O24579	Q6L9M8		Q0DEV5	Q9LKK6	F2X677-1	Q9CAD0	Q9ZNV0	Q84T92	no protein	P10388	P14712		O24579 and Q9FR09	O24579 and Q9FR09		Q0DEV5	A6YQX6	Q655Y0																		A0A0S0G7V0	B9A1G4	A4GRU8	P11511	Q8L3Y5	O54693	P46684	O76858	Q9V674	Q9V674	Q8INI8	Q8INI8	Q8INI8	P17276	P13706	P61851	P23023	P09957	O60882	P14091	P00687	P00687	P00687	P00687	P02557	Q6U6J0	P49085	Q06F33	Q04671	O22045	O22045	Q9VMT5	Q9VYX5	Q03378	A0A077DF90	Q8L699	Q8L699	Q8L699	Q8L699	Q8L699	Q8L699	Q6L973	Q6L973	Q6L973	Q3SYK4	Q9C035	Q9C035	B1N669	P55241	H6U1F1	H6U1F1	O64973	Q8S483	P01236	P12959	P0CX80	Q40253	P05532	O49163	A0A0S0G7V0
11	UniProtKB_Species	Pisum sativum	Mus musculus		Zea mays							Ipomoea purpurea	Oryza sativa	A.thaliana				Zea mays	Zea mays		Zea mays		Arabidopsis thaliana																		Helicoverpa armigera	Oryza sativa subsp. japonica	Petunia integrifolia	Homo sapiens	Glycine max	Mus musculus	Mus musculus	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Homo sapiens	Homo sapiens	Mus musculus	Mus musculus	Mus musculus	Mus musculus	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Bombyx mori	Zea mays	Cochliobolus heterostrophus	Homo sapiens	Ipomoea nil	Ipomoea nil	Drosophila melanogaster	Drosophila melanogaster	Antirrhinum majus	Vanessa cardui	Setaria italica	Setaria italica	Setaria italica	Setaria italica	Setaria italica	Setaria italica	Vitis vinifera	Vitis vinifera	Vitis vinifera	Mus musculus	Homo sapiens	Homo sapiens	Solanum lycopersicum	Zea mays	Citrus sinensis	Citrus sinensis	Arabidopsis thaliana	Zea mays	Homo sapiens	Zea mays	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Linum usitatissimum	Mus musculus	Zea mays	Helicoverpa armigera
12	String		10090.ENSMUSP00000005815																																									9606.ENSP00000379683		10090.ENSMUSP00000109409	10090.ENSMUSP00000034927		7227.FBpp0087100	7227.FBpp0087100	7227.FBpp0082107	7227.FBpp0082107	7227.FBpp0082107	7227.FBpp0076523	7227.FBpp0305431	7227.FBpp0305736	7227.FBpp0303107	7227.FBpp0070070	9606.ENSP00000260228	9606.ENSP00000350911	10090.ENSMUSP00000070368	10090.ENSMUSP00000070368	10090.ENSMUSP00000070368	10090.ENSMUSP00000070368	4932.YFL037W	7091.BGIBMGA013930-TA	4577.GRMZM2G300348_P02		9606.ENSP00000346659			7227.FBpp0078698	7227.FBpp0073359									29760.VIT_02s0033g00410.t01	29760.VIT_02s0033g00410.t01	29760.VIT_02s0033g00410.t01	10090.ENSMUSP00000093207	9606.ENSP00000369373	9606.ENSP00000369373	4081.Solyc10g079240.1.1	4577.GRMZM2G429899_P01			3702.AT1G12220.1		9606.ENSP00000302150	4577.GRMZM2G015534_P01	4932.YHR055C		10090.ENSMUSP00000005815
13	Sequence Similarities	Belongs to the glycosyl hydrolase 13 family. GlgB subfamily.	Belongs to the protein kinase superfamily. Tyr protein kinase family. CSF-1/PDGF receptor subfamily.																																							Belongs to the disease resistance NB-LRR family.		Belongs to the cytochrome P450 family.		Belongs to the tumor necrosis factor family.	Belongs to the GLI C2H2-type zinc-finger protein family.		Belongs to the cytochrome P450 family.	Belongs to the cytochrome P450 family.	Belongs to the heat shock protein 70 family.	Belongs to the heat shock protein 70 family.	Belongs to the heat shock protein 70 family.	Belongs to the biopterin-dependent aromatic amino acid hydroxylase family.	Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family.	Belongs to the Cu-Zn superoxide dismutase family.		Belongs to the major royal jelly protein family.	Belongs to the peptidase M10A family.	Belongs to the peptidase A1 family.	Belongs to the glycosyl hydrolase 13 family.	Belongs to the glycosyl hydrolase 13 family.	Belongs to the glycosyl hydrolase 13 family.	Belongs to the glycosyl hydrolase 13 family.	Belongs to the tubulin family.	Belongs to the peptidase S33 family.	Belongs to the phytoene/squalene synthase family.		Belongs to the CitM (TC 2.A.11) transporter family.	Belongs to the chalcone/stilbene synthases family.	Belongs to the chalcone/stilbene synthases family.	Belongs to the cytochrome P450 family.			Belongs to the Wnt family.	Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.	Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.	Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.	Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.	Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.	Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.				Belongs to the vertnin family.	Belongs to the TRIM/RBCC family.	Belongs to the TRIM/RBCC family.		Belongs to the bacterial/plant glucose-1-phosphate adenylyltransferase family.			Belongs to the disease resistance NB-LRR family.		Belongs to the somatotropin/prolactin family.	Belongs to the bZIP family.	Belongs to the metallothionein superfamily. Type 12 family.		Belongs to the protein kinase superfamily. Tyr protein kinase family. CSF-1/PDGF receptor subfamily.
14	Synonyms		W;Bs;Fdc;Ssm;SCO1;SCO5;SOW3;CD117;c-KIT;Tr-kit;Gsfsco1;Gsfsco5;Gsfsow3;Sl		P;GRMZM2G084799																																							ARO;ARO1;CPV1;CYAR;CYP19;CYPXIX;P-450AROM	Rfs2;Rhg1;rhg1g	Ta;Ed1;HED;EDA1;XLHED;tabby;Eda-A1;Eda-A2;Tnlg7c	ZIC;ZNF201;Zic	ebony;CG3331	6g1;anon-WO03025223.16;anon-WO03025223.17;CG8453;Cyp6-like;cyp6g1;Cyp6G1;CYP6g1;CYP6G1;Cyp6gl;DDT-R;Dmel-Cyp6g1;Dmel\CG8453;RDDT;RI;RI[DDT];RI[II];Rst(2)DDT;CYP6-like	6g1;anon-WO03025223.16;anon-WO03025223.17;CG8453;Cyp6-like;cyp6g1;Cyp6G1;CYP6g1;CYP6G1;Cyp6gl;DDT-R;Dmel-Cyp6g1;Dmel\CG8453;RDDT;RI;RI[DDT];RI[II];Rst(2)DDT;CYP6-like	CG31449;dhsp70;dHsp70;Dm-hsp70;Dmel\CG31449;Hsp 70;hsp-70;Hsp-70;hsp70;Hsp70;HSP70;hsp70 87C;hsp70 Ba;Hsp70(87C);hsp70b;hsp70B;Hsp70B;hsp70ba;hsp70Ba	CG31449;dhsp70;dHsp70;Dm-hsp70;Dmel\CG31449;Hsp 70;hsp-70;Hsp-70;hsp70;Hsp70;HSP70;hsp70 87C;hsp70 Ba;Hsp70(87C);hsp70b;hsp70B;Hsp70B;hsp70ba;hsp70Ba	CG31449;dhsp70;dHsp70;Dm-hsp70;Dmel\CG31449;Hsp 70;hsp-70;Hsp-70;hsp70;Hsp70;HSP70;hsp70 87C;hsp70 Ba;Hsp70(87C);hsp70b;hsp70B;Hsp70B;hsp70ba;hsp70Ba	bu;CG7399;Dmel\CG7399;DTPH;DTPHu;pah;Pah;PAH;Tph;TpH;TPH;Trh;TRH	GPD;alpha-GPD;alpha-Gpdh;alpha-GPDH;alpha-GPDH-1;alphaGpd;alphaGpdh;alphaGPDH;alphaGpdh-1;CG9042;dGpdh;Dmel\CG9042;DmG3PDH;DROGPDHA;G3pdh;G3PDH;GAPDH;Gdh;Gpd;GPDA;gpdh;Gpdh;GPDH;gpdh-1;GPDH-1;sn-Gpdh	Cu;24492;CG11793;cSod;cSOD;Cu-Zn SOD;Cu/Zn sod;Cu/Zn SOD;Cu/Zn superoxide dismutase;Cu/ZnSOD;CuSOD;CuZn SOD;CuZn-SOD;CuZn-SOD1;CuZnSOD;Cu[2+]/Zn[2+]SOD;Dmel\CG11793;dsod;dSOD1;G;l(3)108;l(3)68Af';l(3)G;Mn SOD;sod;Sod;SOD;Sod-1;SOD-1;sod1;SOD1;SODC_DROME;To;To-1;Zn Sod;Zn SOD;Zn-SOD;ZnSod	CG11094;Dmdsx;Dmel\CG11094;Dsx;DSX;dsxF;dsxM;Hr;ix-62c	CG3757;Dmel\CG3757;EG:125H10.2;T6;Y	AI2A2;MMP-20	CATE	Amy-1;Amy1a;C030014B17Rik;Amy-1-a	Amy-1;Amy1a;C030014B17Rik;Amy-1-a	Amy-1;Amy1a;C030014B17Rik;Amy-1-a	Amy-1;Amy1a;C030014B17Rik;Amy-1-a	ARM10;SHE8;YFL037W	JHEH;bommo-JHEH	pb1;PSY1;ZmPSY1;GRMZM2G300348;Y1;ZEAMMB73_Zm00001d036345		P;SHEP1;BEY;PED;BEY1;BEY2;BOCA;EYCL;HCL3;EYCL2;EYCL3;D15S12	CHSD;CHS-D	CHSD;CHS-D	28d1;CG10833;Dmel\CG10833	Dmel\CG11699;CG11699;Dmel_CG11699			GBSSI	GBSSI	GBSSI	GBSSI	GBSSI	GBSSI	mybA;MybA3;mybA1;VVMYBA1;VvmybA3;MYBA1;VIT_02s0033g00410	mybA;MybA3;mybA1;VVMYBA1;VvmybA3;MYBA1;VIT_02s0033g00410	mybA;MybA3;mybA1;VVMYBA1;VvmybA3;MYBA1;VIT_02s0033g00410	7420416P09Rik	RNF88;TRIM5alpha	RNF88;TRIM5alpha	SUN;LYC_68t000013;SUNLYC_67t000009	shrunken-2;GRMZM2G429899			DISEASE RESISTANCE PROTEIN RPS5;RESISTANT TO P. SYRINGAE 5;T28K15.5;T28K15_5;At1g12220	Z138B04_Z333J11.11	GHA1		CUP1;MTH1;YHR053C		W;Bs;Fdc;Ssm;SCO1;SCO5;SOW3;CD117;c-KIT;Tr-kit;Gsfsco1;Gsfsco5;Gsfsow3;Sl	GRMZM5G881887
15	GO Molecular	GO:0043169;GO:0004553;GO:0003844;GO:0102752	GO:0004888;GO:0005524;GO:0042803;GO:0046872;GO:0002020;GO:0004714;GO:0004713;GO:0019955;GO:0005020		GO:0003677													GO:0003677	GO:0003677																						GO:0005524;GO:0042626	GO:0043531	GO:0003677	GO:0020037;GO:0005506;GO:0070330;GO:0009055;GO:0016712;GO:0008395;GO:0019825	GO:0005524;GO:0004672	GO:0038177;GO:0005123;GO:0005164	GO:0001228;GO:0003700;GO:0000977;GO:0046872;GO:0000981;GO:0000978	GO:0000036;GO:0003833;GO:0031177	GO:0020037;GO:0005506;GO:0004497;GO:0016705	GO:0020037;GO:0005506;GO:0004497;GO:0016705	GO:0005524;GO:0031072;GO:0051082;GO:0016887;GO:0042623;GO:0051787;GO:0044183	GO:0005524;GO:0031072;GO:0051082;GO:0016887;GO:0042623;GO:0051787;GO:0044183	GO:0005524;GO:0031072;GO:0051082;GO:0016887;GO:0042623;GO:0051787;GO:0044183	GO:0005506;GO:0004505;GO:0004510	GO:0042803;GO:0051287;GO:0004367	GO:0042803;GO:0016209;GO:0005507;GO:0004784	GO:0042803;GO:0000977;GO:0008270;GO:0001077;GO:0001078		GO:0004222;GO:0008270	GO:0042803;GO:0004190;GO:0008233	GO:0004556;GO:0103025;GO:0005509;GO:0016160;GO:0031404	GO:0004556;GO:0103025;GO:0005509;GO:0016160;GO:0031404	GO:0004556;GO:0103025;GO:0005509;GO:0016160;GO:0031404	GO:0004556;GO:0103025;GO:0005509;GO:0016160;GO:0031404	GO:0005525;GO:0003924;GO:0005200	GO:0033961	GO:0004310;GO:0016767;GO:0046905;GO:0051996	GO:0008270;GO:0003677;GO:0000981	GO:0005215;GO:0005302	GO:0016210	GO:0016210	GO:0020037;GO:0005506;GO:0004497;GO:0016705		GO:0046983;GO:0003700;GO:0000977	GO:0005102	GO:0004373	GO:0004373	GO:0004373	GO:0004373	GO:0004373	GO:0004373	GO:0003677	GO:0003677	GO:0003677		GO:0042802;GO:0042803;GO:0008270;GO:0019901;GO:0030674;GO:0008329;GO:0004842	GO:0042802;GO:0042803;GO:0008270;GO:0019901;GO:0030674;GO:0008329;GO:0004842		GO:0005524;GO:0008878	GO:0003677	GO:0003677	GO:0005524;GO:0042802;GO:0000166;GO:0043531;GO:0038023	GO:0046983	GO:0005179;GO:0005148	GO:0003700;GO:0003677	GO:0016209;GO:0005507;GO:0046870;GO:0004784	GO:0043531	GO:0004888;GO:0005524;GO:0042803;GO:0046872;GO:0002020;GO:0004714;GO:0004713;GO:0019955;GO:0005020	GO:0050662;GO:0003824	GO:0005524;GO:0042626
16	GO Cellular	GO:0009501;GO:0009507	GO:0005886;GO:0005737;GO:0005887;GO:0043235;GO:0005615;GO:0009986;GO:0009898;GO:0009897;GO:0001669;GO:0005911;GO:0042629		GO:0005634													GO:0005634	GO:0005634																						GO:0016021		GO:0005634	GO:0016021;GO:0016020;GO:0005783;GO:0005789	GO:0016021	GO:0005887;GO:0005576;GO:0005789;GO:0045177;GO:0005581;GO:0005811	GO:0005737;GO:0005634	GO:0005737	GO:0005789;GO:0031090	GO:0005789;GO:0031090	GO:0005737;GO:0005829	GO:0005737;GO:0005829	GO:0005737;GO:0005829		GO:0005829;GO:0030018;GO:0009331;GO:0031430	GO:0005737;GO:0005829;GO:0005634;GO:0005777	GO:0005634	GO:0005737;GO:0005576;GO:0070451	GO:0005576;GO:0031012;GO:0005615	GO:0005768	GO:0005615	GO:0005615	GO:0005615	GO:0005615	GO:0005737;GO:0005874;GO:0005816;GO:0005881;GO:0005828;GO:0005880;GO:0045298	GO:0016021;GO:0005789;GO:0031090	GO:0010287	GO:0005634	GO:0016021;GO:0005737;GO:0010008;GO:0005789;GO:0005765;GO:0033162			GO:0005789;GO:0031090	GO:0016021	GO:0005634	GO:0005576	GO:0009501;GO:0009507	GO:0009501;GO:0009507	GO:0009501;GO:0009507	GO:0009501;GO:0009507	GO:0009501;GO:0009507	GO:0009501;GO:0009507	GO:0005634	GO:0005634	GO:0005634		GO:0005737;GO:0005829;GO:0005634;GO:0000932	GO:0005737;GO:0005829;GO:0005634;GO:0000932		GO:0009501;GO:0009507	GO:0005634	GO:0005634	GO:0005886		GO:0005576;GO:0005615;GO:0030141;GO:0031904	GO:0005634	GO:0005829		GO:0005886;GO:0005737;GO:0005887;GO:0043235;GO:0005615;GO:0009986;GO:0009898;GO:0009897;GO:0001669;GO:0005911;GO:0042629		GO:0016021
17	GO Biological	GO:0019252;GO:0005978;GO:0009793	GO:0043066;GO:0030154;GO:0043473;GO:0070374;GO:0035234;GO:0035162;GO:0008584;GO:0001541;GO:0008284;GO:0043406;GO:0010628;GO:0043410;GO:0007283;GO:0008360;GO:0048070;GO:0006468;GO:0060326;GO:0006935;GO:0048565;GO:0006954;GO:0019221;GO:0048863;GO:0048066;GO:0030318;GO:0009968;GO:0046777;GO:0030218;GO:0018108;GO:0097067;GO:1904349;GO:0000187;GO:0046427;GO:0042531;GO:0030335;GO:0046686;GO:0035556;GO:0031532;GO:0002371;GO:0050910;GO:0050673;GO:0038162;GO:0038093;GO:0007281;GO:0008354;GO:0006687;GO:0035701;GO:0030097;GO:0002327;GO:0038109;GO:0030032;GO:0002320;GO:0002551;GO:0032762;GO:0043303;GO:0060374;GO:0035855;GO:0097326;GO:0097324;GO:0002573;GO:0002318;GO:0043069;GO:1904343;GO:0051091;GO:0048170;GO:0045747;GO:0031274;GO:0120072;GO:1905065;GO:1904251;GO:0009314;GO:0048103;GO:0035019;GO:0007286;GO:0030217;GO:0043586;GO:0008542																																									GO:0060736;GO:0016125;GO:0008585;GO:0030879;GO:0006694;GO:0030540;GO:0006710;GO:0006703;GO:0002677;GO:0010760;GO:2000866;GO:0061370;GO:0060065		GO:0006955;GO:0030154;GO:0043473;GO:0010628;GO:0051092;GO:0019221;GO:0007160;GO:0010467;GO:0001942;GO:0060789;GO:0042475;GO:0090263;GO:0043123;GO:1901224;GO:1901222;GO:0060662;GO:0043588;GO:0061153	GO:0007417;GO:0045944;GO:0030154;GO:0001501;GO:0045893;GO:0007420;GO:0042472;GO:0008589;GO:0007389;GO:0042307;GO:0021510;GO:0007628	GO:0048085;GO:0042417;GO:0007623;GO:0048082;GO:0048066;GO:0043042;GO:0007593;GO:0048067;GO:0001692;GO:0045475;GO:0006583;GO:0048022;GO:0042440	GO:0046680;GO:0017085;GO:0046701;GO:0046689;GO:0046683	GO:0046680;GO:0017085;GO:0046701;GO:0046689;GO:0046683	GO:0001666;GO:0034605;GO:0009408;GO:0034620;GO:0051085;GO:0035080;GO:0042026;GO:0006986	GO:0001666;GO:0034605;GO:0009408;GO:0034620;GO:0051085;GO:0035080;GO:0042026;GO:0006986	GO:0001666;GO:0034605;GO:0009408;GO:0034620;GO:0051085;GO:0035080;GO:0042026;GO:0006986	GO:0007616;GO:0006726;GO:0006559;GO:0042427;GO:0006571	GO:0005975;GO:0006067;GO:0055114;GO:0006641;GO:0055093;GO:0007629;GO:0046168;GO:0006072;GO:0006650;GO:0006116	GO:0008340;GO:0007568;GO:0006979;GO:0019430;GO:0001306;GO:0048167;GO:1903146;GO:2000331	GO:0045944;GO:0006357;GO:0007530;GO:0045892;GO:0045893;GO:0046660;GO:0048086;GO:0048071;GO:0035215;GO:0007485;GO:0016199;GO:0007619;GO:0045497;GO:0019101;GO:0007486;GO:0045496;GO:0008049;GO:0045433;GO:0046661;GO:0045498;GO:0018993	GO:0042438;GO:0048082;GO:0048066;GO:0048067;GO:0006583;GO:0048065;GO:0060179	GO:0030198;GO:0006508;GO:0030163;GO:0030574;GO:0022617;GO:0097186;GO:0070173	GO:0006508;GO:0019886;GO:0016540;GO:0030163	GO:0009617;GO:0016052	GO:0009617;GO:0016052	GO:0009617;GO:0016052	GO:0009617;GO:0016052	GO:0007010;GO:0000278;GO:0000070;GO:0007017;GO:0046677;GO:0000226;GO:0045143;GO:0030473;GO:0090316	GO:0019439	GO:0006696;GO:0016117	GO:0006351	GO:0042438;GO:0008283;GO:0030318;GO:0007286;GO:0006726	GO:0009813	GO:0009813			GO:0007275;GO:0045944	GO:0007275;GO:0016055	GO:0019252	GO:0019252	GO:0019252	GO:0019252	GO:0019252	GO:0019252					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	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		GO:0019252;GO:0005978			GO:0006952;GO:0008219;GO:0009816;GO:0009626		GO:0044267;GO:0001937;GO:0008283;GO:0008284;GO:0050679;GO:0007565;GO:0032496;GO:0007623;GO:0032355;GO:0007166;GO:0040014;GO:0045471;GO:0060397;GO:0046427;GO:0030879;GO:0007595;GO:0033555;GO:0016525;GO:0042698;GO:0007567;GO:1903489;GO:1902895;GO:0030278;GO:0007584;GO:0031667		GO:0071585;GO:0010273;GO:0046688;GO:0019430	GO:0007165	GO:0043066;GO:0030154;GO:0043473;GO:0070374;GO:0035234;GO:0035162;GO:0008584;GO:0001541;GO:0008284;GO:0043406;GO:0010628;GO:0043410;GO:0007283;GO:0008360;GO:0048070;GO:0006468;GO:0060326;GO:0006935;GO:0048565;GO:0006954;GO:0019221;GO:0048863;GO:0048066;GO:0030318;GO:0009968;GO:0046777;GO:0030218;GO:0018108;GO:0097067;GO:1904349;GO:0000187;GO:0046427;GO:0042531;GO:0030335;GO:0046686;GO:0035556;GO:0031532;GO:0002371;GO:0050910;GO:0050673;GO:0038162;GO:0038093;GO:0007281;GO:0008354;GO:0006687;GO:0035701;GO:0030097;GO:0002327;GO:0038109;GO:0030032;GO:0002320;GO:0002551;GO:0032762;GO:0043303;GO:0060374;GO:0035855;GO:0097326;GO:0097324;GO:0002573;GO:0002318;GO:0043069;GO:1904343;GO:0051091;GO:0048170;GO:0045747;GO:0031274;GO:0120072;GO:1905065;GO:1904251;GO:0009314;GO:0048103;GO:0035019;GO:0007286;GO:0030217;GO:0043586;GO:0008542
18	GenBankID	X80009			EF165349																		AB292777																	AUG71567		AB379815.1			JN597009																					Q7KB18				AB004905	AB004905	33749	32101			AB089141	AB089141	AB089141	AB089141	AB089141	AB089141	FN596505	DQ886418	FN596505	BAJ11938	AAB33697	AAT73777	EF094939	M81603	JN402330	JN402330	U97221	AF466202	AAZ82304	X16618	K02204	U27081		AF041043
19	Trait Category	Physiology &2 Morphology	Morphology	Physiology	Morphology	Morphology	Morphology	Physiology	Physiology	Morphology	Morphology	Morphology	Morphology	Morphology	Physiology	Physiology	Morphology	Morphology	Morphology	Morphology	physiology	Morphology	Morphology and Physiology			Morphology and Physiology														Morphology	Physiology	Physiology	MorphologyPhysiology	Morphology	Physiology	Morphology &2 Morphology &3 Morphology	Morphology &2 Morphology	Morphology	Physiology	Physiology	Physiology	Physiology	Physiology	Physiology	Physiology	Physiology	Morphology	Morphology	Physiology	Physiology	Physiology	Physiology	Physiology	Physiology	Physiology	Physiology	Physiology	Physiology &2 Physiology	Morphology	Morphology	Morphology	Physiology	Physiology	Morphology	Morphology	Physiology	Physiology	Physiology	Physiology	Physiology	Physiology	Morphology	Morphology	Morphology	Morphology	Physiology	Physiology	Morphology	Physiology	Morphology	Morphology	Physiology	Morphology	Physiology	Physiology	Physiology	Physiology	Morphology	Physiology	Physiology
20	Trait	Starch structure &2 Seed aspect	Coloration (coat)	Copulatory plug	Coloration (seed)	Coloration (fruit)	Coloration (fruit)	Starch structure	Oleate level	Coloration (seed)	Coloration (flower)	Flower coloration	Coloration (hull and internode)	flower organization +fruit fertility	The high molecular weight (HMW) glutenin content	Photoperiod sensitivity	Flower Morphology	colorless fernel pericarp and cob	Orange kernels and cob glume	Coloration (Flower tube)	Amount of amylose	Inflorescence architecture	Suppression of the development of spikelets suppresses precocious conversion of rachis branch meristems to spikelets to ensure generation of certain number of spikelets			coloring observed in the coat of the domestic dog and is characterized by patches of diluted pigment+impaired function of the auditory and ophthalmologic systems (Waardenburg-like syndrom														Coloration (bulb)	Xenobiotic resistance (insecticide; Bt Cry2Ab toxin)	Pathogen resistance (rice blast disease; fungal pathogen; Magnaporthe grisea)	Coloration (anthocyanin accumulation in entire plant)	Coloration (feathers)	Pathogen resistance (cyst nematode)	Scales (loss) &2 Femoral glands (absent) &3 Tooth number	Fin morphology (skeleton; dorsal fin; caudal fin) &2 Pigmentation (ventralized trunk)	Coloration (abdomen; male)	Xenobiotic resistance (insecticide)	Xenobiotic resistance (insecticide)	Temperature tolerance	Temperature tolerance	Temperature tolerance	Enzymatic activity	Enzymatic activity	Xenobiotic resistance (paraquat)	Coloration (wing ; Batesian mimicry)	Coloration (body; wing)	Tooth absence (no enamel production)	Digestion (absence of stomach)	Starch processing	Starch processing	Starch processing	Starch processing	Xenobiotic resistance (benzimidazole)	Oxidative stress resistance	Carotenoid content (fruit)	Xenobiotic resistance (fungicide) &2 Melanin content	Coloration (albinism)	Coloration (flower)	Coloration (flower)	Xenobiotic resistance (nicotine ; larval stage)	Xenobiotic resistance	Flower morphology (anther elevation)	Coloration (wing; Batesian mimicry)	Amylose content	Amylose content	Amylose content	Amylose content	Amylose content	Amylose content	Coloration (fruit)	Coloration (fruit)	Coloration (fruit)	Vertebrae number	Pathogen resistance (retroviruses)	Pathogen resistance (retroviruses)	Fruit shape	Feather	Coloration (fruit; cold-dependent)	Coloration (fruit; cold-dependent)	Pathogen resistance	Coloration (seeds)	Gene expression change (quantitative; increase)	Lysine content (endosperm)	Low-glucose adaptation (experimental evolution)	Pathogen resistance	Coloration (coat)	Pathogen resistance	Xenobiotic resistance (insecticide; Bt Cry1Ac toxin)
21	State A	Pisum sativum smooth &2	Felis catus - white-spotted	C. elegans - copulatory plug	Zea mays - allele P-RR	Vitis vinifera - red berries	red seed	Oryza sativa - Normal Starch composition	Arachis hypogaea (Peanut) normal oleate level	Brassica rapa - Black seeds	Dark‐purple flowers, dark-brown seeds	Ipomoea tricolor cultivar Heavenly Blue - bright blue flowers	Oryza sativa green hull and internode	WT : small size fruit		Photoperiod sensitive soybean	Ipomoea nil-internal organs consist in five stamen and one pistil, comprised in three carpels	Zea mays - allele P -vv9D9A	Zea mays - allele P -RR11	Antirrhinum majus JI: 98	Zea mays - wx-m1	Vitis vinifera 'Carignan'-wild type																		yellow bulb	Trichoplusia ni - Bt-Cry2Ab susceptible	sensitive	C. annuum	wild-type	Glycine max - sensitive	bearded dragons &2 bearded dragons &3 bearded dragons	wild-type – wedge shaped body morphology; small dorsal fin; asymmetric caudal fin &2 wild-type - lack of bright pigmentation on the back	dark posterior male abdomen	Drosophila simulans - susceptible	Drosophila simulans - susceptible	Drosophila melanogaster - wild-type tolerance	Drosophila melanogaster - wild-type tolerance	Drosophila melanogaster - wild-type tolerance	Drosophila melanogaster - wild-type	Drosophila melanogaster - wild-type activity	Drosophila melanogaster	non-mimetic female	population of Drosophila melanogaster from Uman (Ukraine) - wild-type	presence of teeth	presence of stomach and gastric acid production	Owl monkey and Marmoset	Sus scrofa	Rattus norvegicus	Mus musculus	sensitive	Drosophila melanogaster	red flesh	high melanin levels - lower growth rate in absence of funcicide - higher growth rate in presence of fungicide &2 high melanin levels - lower growth rate in absence of funcicide - higher growth rate in presence of fungicide	Corn snake with black borders	Common morning glory with white flower with variegated colored flakes and sectors (KK/VR-37 & KK/VR-40a & KK/VP-347 & YY/VP-SU2001 & KK/WR-321)	Common morning glory with colored flower (YO/FR-34 & KK/FR-35 & KK/FP-36 & YO/FP-39)	Drosophila melanogaster susceptible to nicotine	Drosophila melanogaster common wild type	Primula vulgaris	Limenitis arthemis arthemis - White Admiral (with White Band)	Setaria italica waxy landraces	Setaria italica ssp. Viridis (wild)	Setaria italica ssp. Viridis (wild)	Setaria italica ssp. Viridis (wild)	Setaria italica ssp. Viridis (wild)	Setaria italica low-amylose landraces	Vitis vinifera - white-skinned cultivar - VvmybA1a allele	Vitis vinifera - Syrah	Vitis vinifera - red-skinned original VvmybA1 allele	Sus scrofa	Other Old World Monkeys (no HIV-1 restriction activity)	Other New World Monkeys (no HIV-1 restriction activity)	Solanum pimpinellifolium	Zea mays - allele Sh2	Citrus spp. - blond	Citrus spp. - blond	Arabidopsis thaliana- Col0 - resistant	Zea mays ssp. Mays - white seeds	Other primates	Zea mays - hard translucent endosperm	Saccharomyces cerevisiae	Linum usitatissimum	Felis catus	Zea mays - resistant	Helicoverpa armigera - Bt-Cry1Ac susceptible
22	State B	Pisum sativum wrinkled &2	Felis catus - Dominant White/blue iris	C. elegans - no copulatory plug	Zea mays - allele P-VV	Vitis vinifera - white berries	candystripe seed	Oryza sativa japonica subsepcies- Absence of amylose	Arachis hypogaea (Peanut) high oleate level	Brassica rapa - Yellow seeds	White flowers with a colored spot in each ray, ivory seeds	Ipomoea tricolor cultivar Pearly Stable - white flowers	Oryza sativa reddish-brown hull and internode	TE in MIR172p : early fruit development, lack of ethamins, fused sepals, large size seedless fruit		Photoperiod insensitive soybean	Ipomea nil- dp mutant-stamens substituted with petals and carpel with a new flower	Zea mays - allele P-ww2	Zea mays - allele P-oo	Antirrhinum majus JI: 531	Zea mays - wx-m1 S5 and S9 germial derivates	Vitis vinifera 'Carignan', reiterated reproductive meristems (RRM) variant																		white bulb - recessive allele	Trichoplusia ni - Bt-Cry2Ab resistant	resistant	C. annuum KC00134 - purple flowers; leaves; fruits	Henny feathering - dominant mutation that transforms male-specific plumage to female-like plumage	Glycine max - resistant - Rhg1a haplotype - "Peking-type" low-copy number; three or fewer Rhg1 repeats	scaleless bearded dragons - homozygotes lack all scales on the body (ventral/dorsal scales and lateral spines) and femoral glands ; they also exhibit reduced dentition and (paradoxically) longer claws at birth &2 scaleless bearded dragons - homozygotes lack all scales on the body (ventral/dorsal scales and lateral spines) and femoral glands ; they also exhibit reduced dentition and (paradoxically) longer claws at birth &3 scaleless bearded dragons - homozygotes lack all scales on the body (ventral/dorsal scales and lateral spines) and femoral glands ; they also exhibit reduced dentition and (paradoxically) longer claws at birth	Tear-drop shaped body morphology; shape of dorsal fin resembles shape of anal fin; symmetric caudal fin &2 bright pigmentation on back	light posterior male abdomen	Drosophila simulans - resistant	Drosophila simulans - resistant	Drosophila melanogaster - lower tolerance - Arv/Zim allele	Drosophila melanogaster - lower tolerance - Evolution Canyon allele	Drosophila melanogaster - lower tolerance	Drosophila melanogaster - reduced activity	Drosophila melanogaster - reduced activity	Drosophila melanogaster - hypersensitive to paraquat - CA1 allele	female mimetic to distantly related and toxic swallowtails in the genera Pachliopta and Atrophaneura	population of Drosophila melanogaster from Uman (Ukraine) - yellow body and yellow wings	absence of teeth	loss of stomach and no gastric acid production	Capuchin	Sus scrofa	Rattus norvegicus	Mus musculus	resistant	Drosophila melanogaster	yellow flesh	low melanin levels - higher growth rate in absence of funcicide &2 low melanin levels - higher growth rate in absence of funcicide	Amelanistic corn snake with white borders	Common morning glory with stable white flower (KK/WP-3)	Common morning glory with white flower with variegated colored flakes and sectors (KK/VR-37 & KK/VR-40a & KK/VP-347 & YY/VP-SU2001 & KK/WR-321)	Drosophila melanogaster resistant to nicotine	Drosophila melanogaster with increased resistance to benzaldehyde and carbofuran insecticide	Primula vulgaris	Limenitis arthemis astyanax - Red Spotted Purple (melanic morph without a white band ; mimic of Pipevine Swallowtail in southern range of the species distribution)	Setaria italica low-amylose landraces	Setaria italica waxy landraces	Setaria italica waxy landraces	Setaria italica low-amylose landraces	Setaria italica waxy landraces	Setaria italica waxy landraces	Vitis vinifera - red-skinned cultivar - VvmybA1b allele	Vitis vinifera - Grenache	Vitis vinifera - white-skinned cultivar - VvmybA1a allele	Sus scrofa	Macaca spp. (HIV-1 restriction activity)	Aotus spp. (HIV-1 restriction activity)	Solanum lycopersicum "Sun1642"	Zea mays - allele sh2-m1	Citrus sinensis - Sicilian blood oranges	Citrus sinensis - Chinese blood orange	Arabidopsis thaliana- Ler-0 sensitive	Zea mays ssp. Mays - blue seeds - R-Navajo (R-nj) allele	great Apes	Zea mays - soft opaque endosperm with lysine contents - allele o2-m_______	Saccharomyces cerevisiae	Linum usitatissimum	Felis catus - white-spotted	Zea mays - Pr - sensitive	Helicoverpa armigera - Bt-Cry1Ac resistant
23	Taxon A ID	3888	9685	6239	4577	29760	4558	39947	3818	3711	4121	89664	4530	3702	37682	3847	35883	4577	4577		4577	755350	3702			9615														4679	7111	4530	4072	9031	3847	103695	8090	7245	7240	7240	7227	7227	7227	7227	7227	7227	76198	7227	9755	13616 &2 9606	9505 &2 9483	9823	10116	10090	6239	7227	4081	1047171	94885	4121	4121	7227	7227	175104	124411	4555	4555	4555	4555	4555	4555	29760	29760	29760	9823	9527	9479	4084	4577	2706	2706	3702	4577	9443	4577	4932	4006	9685	4577	29058
24	Latin Name A	Pisum sativum	Felis catus	Caenorhabditis elegans	Zea mays									Arabidopsis thaliana																										Allium cepa	Trichoplusia ni	Oryza sativa	Capsicum annuum	Gallus gallus	Glycine max	Pogona vitticeps	Oryzias latipes	Drosophila yakuba	Drosophila simulans	Drosophila simulans	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Papilio memnon	Drosophila melanogaster	Physeter catodon	Monodelphis domestica &2 Homo sapiens	Aotus trivirgatus &2 Callithrix jacchus	Sus scrofa	Rattus norvegicus	Mus musculus	Caenorhabditis elegans	Drosophila melanogaster	Solanum lycopersicum	Zymoseptoria tritici	Pantherophis guttatus	Ipomoea purpurea	Ipomoea purpurea	Drosophila melanogaster	Drosophila melanogaster	Primula vulgaris	Limenitis arthemis	Setaria italica	Setaria italica	Setaria italica	Setaria italica	Setaria italica	Setaria italica	Vitis vinifera	Vitis vinifera	Vitis vinifera	Sus scrofa	Cercopithecidae	Platyrrhini	Solanum pimpinellifolium	Zea mays	Citrus	Citrus	Arabidopsis thaliana	Zea mays	Primates	Zea mays	Saccharomyces cerevisiae	Linum usitatissimum	Felis catus	Zea mays	Helicoverpa armigera
25	Common Name A	pea	domestic cat											thale cress																										onion	cabbage looper	rice		chicken	soybean	central bearded dragon	Japanese medaka				fruit fly	fruit fly	fruit fly	fruit fly	fruit fly	fruit fly		fruit fly	sperm whale	gray short-tailed opossum &2 human	douroucouli &2 white-tufted-ear marmoset	pig	Norway rat	house mouse		fruit fly	tomato			common morning-glory	common morning-glory	fruit fly	fruit fly		white admiral	foxtail millet	foxtail millet	foxtail millet	foxtail millet	foxtail millet	foxtail millet	wine grape	wine grape	wine grape	pig	Old World monkeys	New World monkeys					thale cress				baker's yeast	flax	domestic cat		cotton bollworm
26	Rank A	species	species	species	species									species																										species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species &2 species	species &2 species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	family	parvorder	species	species	genus	genus	species	species	order	species	species	species	species	species	species
27	Taxon A Lineage	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; Hologalegina; IRL clade; Fabeae; Pisum	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; Felinae; Felis	cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea																																			cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; Liliopsida; Petrosaviidae; Asparagales; Amaryllidaceae; Allioideae; Allieae; Allium	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; Noctuoidea; Noctuidae; Plusiinae; Trichoplusia	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Capsiceae; Capsicum	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; Galloanserae; Galliformes; Phasianidae; Phasianinae; Gallus	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	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; Acrodonta; Agamidae; Amphibolurinae; Pogona	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; Atherinomorphae; Beloniformes; Adrianichthyoidei; Adrianichthyidae; Oryziinae; Oryzias	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Papilionidae; Papilioninae; Papilionini; Papilio	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Cetacea; Odontoceti; Physeteridae; Physeter	cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Metatheria; Didelphimorphia; Didelphidae; Didelphinae; Monodelphis &2 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	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; Platyrrhini; Aotidae; Aotus &2 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; Platyrrhini; Cebidae; Callitrichinae; Callithrix; Callithrix	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	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; Rattus	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	cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon	cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Pezizomycotina; leotiomyceta; dothideomyceta; Dothideomycetes; Dothideomycetidae; Capnodiales; Mycosphaerellaceae; Zymoseptoria	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; Colubrinae; Pantherophis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Primulaceae; Primula	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	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Viteae; Vitis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Viteae; Vitis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Viteae; Vitis	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	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	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	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea	cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea	cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum	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; Felinae; Felis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea	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; Noctuoidea; Noctuidae; Heliothinae; Helicoverpa
28	A=Infraspecies	0	0	1	0	1	0	0	0	0	1	1	0	0	1	0	0			0	0	0				0														0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	1	1	1	1	0	0	1	0	1	1	1	1	0	0	1	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0
29	Taxon A Description			C. elegans - several wild isolates		Red grape		Normal rice	Normal Oleate level	black coat seed		cultivar Heavenly Blue with bright blue flower	Oryza sativa - green hull and internode			Glycine max - photoperiod sensitive	I.nil -stamen and pistils as reproductive organs				wx-m1 mutants that show a reduced enzymatic activity of wx gene																																							&2	&2							strain 3D7	Corn snake with black borders	Common morning glory with white flower with variegated colored flakes and sectors (KK/VR-37 & KK/VR-40a & KK/VP-347 & YY/VP-SU2001 & KK/WR-321)	Common morning glory with colored flower (YO/FR-34 & KK/FR-35 & KK/FP-36 & YO/FP-39)	Strain ISO-1			Limenitis arthemis arthemis - White Admiral (with White Band)		Setaria italica ssp. Viridis (wild)	Setaria italica ssp. Viridis (wild)	Setaria italica ssp. Viridis (wild)	Setaria italica ssp. Viridis (wild)			Vitis vinifera - Syrah							Citrus spp. - blond	Citrus spp. - blond	Arabidopsis thaliana- Col0 - resistant	Zea mays ssp. Mays - white seeds
30	Taxon B ID	3888	9685	6239	4577	29760	4558	4530	3818	1813537	4121	89664	4530	3702	4565	3847		4577	4577		4577	755350	3702																	4679	7111	4530	4072	9031	3847	103695	8090	129105	7240	7240	7227	7227	7227	7227	7227	7227	76198	7227	9770 &2 27602 &3 9773	9258	9516	9823	10116	10090	6239	7227	4081	1047171	94885	4121	4121	7227	7227	175104	124411	4555	4555	4555	4555	4555	4555	29760	29760	29760	9825	9539	9504	4081	4577	2711	2711	3702	4577	207598	4577	4932	4006	9685	4577	29058
31	Latin Name B	Pisum sativum	Felis catus	Caenorhabditis elegans	Zea mays									A.thaliana																										Allium cepa	Trichoplusia ni	Oryza sativa	Capsicum annuum	Gallus gallus	Glycine max	Pogona vitticeps	Oryzias latipes	Drosophila santomea	Drosophila simulans	Drosophila simulans	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Drosophila melanogaster	Papilio memnon	Drosophila melanogaster	Balaenoptera physalus &2 Balaena mysticetus &3 Megaptera novaeangliae	Ornithorhynchus anatinus	Cebus capucinus	Sus scrofa	Rattus norvegicus	Mus musculus	Caenorhabditis elegans	Drosophila melanogaster	Solanum lycopersicum	Zymoseptoria tritici	Pantherophis guttatus	Ipomoea purpurea	Ipomoea purpurea	Drosophila melanogaster	Drosophila melanogaster	Primula vulgaris	Limenitis arthemis	Setaria italica	Setaria italica	Setaria italica	Setaria italica	Setaria italica	Setaria italica	Vitis vinifera	Vitis vinifera	Vitis vinifera	Sus scrofa domesticus	Macaca	Aotus	Solanum lycopersicum	Zea mays	Citrus sinensis	Citrus sinensis	Arabidopsis thaliana	Zea mays	Homininae	Zea mays	Saccharomyces cerevisiae	Linum usitatissimum	Felis catus	Zea mays	Helicoverpa armigera
32	Common Name B	pea	domestic cat											thale cress																										onion	cabbage looper	rice		chicken	soybean	central bearded dragon	Japanese medaka				fruit fly	fruit fly	fruit fly	fruit fly	fruit fly	fruit fly		fruit fly	Fin whale &2 bowhead whale &3 humpback whale	platypus	white-faced sapajou	pig	Norway rat	house mouse		fruit fly	tomato			common morning-glory	common morning-glory	fruit fly	fruit fly		white admiral	foxtail millet	foxtail millet	foxtail millet	foxtail millet	foxtail millet	foxtail millet	wine grape	wine grape	wine grape	domestic pig	macaques	night monkeys	tomato		sweet orange	sweet orange	thale cress				baker's yeast	flax	domestic cat		cotton bollworm
33	Rank B	species	species	species	species									species																										species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species &2 species &3 species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	species	subspecies	genus	genus	species	species	species	species	species	species	subfamily	species	species	species	species	species	species
34	Taxon B Lineage	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; Hologalegina; IRL clade; Fabeae; Pisum	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; Felinae; Felis	cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea																																			cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; Liliopsida; Petrosaviidae; Asparagales; Amaryllidaceae; Allioideae; Allieae; Allium	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; Noctuoidea; Noctuidae; Plusiinae; Trichoplusia	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Capsiceae; Capsicum	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; Galloanserae; Galliformes; Phasianidae; Phasianinae; Gallus	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	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; Acrodonta; Agamidae; Amphibolurinae; Pogona	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; Atherinomorphae; Beloniformes; Adrianichthyoidei; Adrianichthyidae; Oryziinae; Oryzias	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Papilionidae; Papilioninae; Papilionini; Papilio	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Cetacea; Mysticeti; Balaenopteridae; Balaenoptera &2 cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Cetacea; Mysticeti; Balaenidae; Balaena &3 cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Cetacea; Mysticeti; Balaenopteridae; Megaptera	cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Prototheria; Monotremata; Ornithorhynchidae; Ornithorhynchus	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; Platyrrhini; Cebidae; Cebinae; Cebus	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	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; Rattus	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	cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon	cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Pezizomycotina; leotiomyceta; dothideomyceta; Dothideomycetes; Dothideomycetidae; Capnodiales; Mycosphaerellaceae; Zymoseptoria	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; Colubrinae; Pantherophis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	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; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Primulaceae; Primula	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	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Viteae; Vitis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Viteae; Vitis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Viteae; Vitis	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	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; Cercopithecidae; Cercopithecinae	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; Platyrrhini; Aotidae	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea	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	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea	cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum	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; Felinae; Felis	cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea	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; Noctuoidea; Noctuidae; Heliothinae; Helicoverpa
35	B=Infraspecies	0	1	1	0	1	0	0	0	1	1	1	0	0	1	1	0			1	0	0																		0	0	1	1	0	0	0	0	0	1	1	1	1	1	0	0	0	0	0	1	0	0	0	0	0	1	0	1	1	1	1	1	1	0	0	1	0	1	1	1	1	0	0	1	0	0	0	0	1	0	1	1	1	1	0	0	0	0	1	1	0
36	Taxon B Description		Felis catus - Dominant White/blue iris	C. elegans - N2		White grape		Glutinous rice	High Oleate level	Indian yellow sarson	Pale pigmented flowers and ivory seeds	cultivar pearly gates with white flowers	Oryza sativa - pigmented hull and internode			Glycine max ssp. soja, restricted region of Northern Japan, photoperiod insensitive	I.nil- petals intead of reproductive organs			JI:98	S5 and S9 derivated mutatns of wx-m1 mutant																					K59	KC00134						Rhone Valley population	California population	The Arv/Zim populations were founded from crosses of parents from California and Zimbabwe and were cultured at 188C for 5 years before experimentation.	flies were collected from the north-facing slope (NFS) of Evolution Canyon (Lower Nahal Oren; Mt. Carmel; Israel) during August–September 1997	T32 population - collected in Chad; Africa in 1977						&2 &3						JU3125		yellow flesh - r[y] mutant	strain 3D1	Corn snake with white borders	Common morning glory with stable white flower (KK/WP-3)	Common morning glory with white flower with variegated colored flakes and sectors (KK/VR-37 & KK/VR-40a & KK/VP-347 & YY/VP-SU2001 & KK/WR-321)	Strain A4			Limenitis arthemis astyanax - Red Spotted Purple (melanic morph without a white band ; mimic of Pipevine Swallowtail in southern range of the species distribution)		Setaria italica waxy landraces	Setaria italica waxy landraces	Setaria italica low-amylose landraces	Setaria italica waxy landraces			Vitis vinifera - Grenache					Solanum lycopersicum "Sun1642"		Citrus sinensis - Sicilian blood oranges	Citrus sinensis - Chinese blood orange	Arabidopsis thaliana- Ler-0 sensitive	Zea mays ssp. Mays - blue seeds - R-Navajo (R-nj) allele					Felis catus - white-spotted	Zea mays - Pr - sensitive
37	Ancestral State	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A		Taxon B	Taxon A	Taxon A	Taxon A	Taxon A		Taxon A		Taxon A																	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Unknown	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Data not curated	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Unknown	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Taxon A	Data not curated	Taxon A	Data not curated	Data not curated	Data not curated	Data not curated	Taxon A	Taxon A	Taxon A	Data not curated	Taxon A	Data not curated	Taxon A	Taxon A	Data not curated	Taxon A	Taxon A	Taxon A
38	Taxonomic Status	Domesticated	Domesticated	Intraspecific	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated		Domisticated	Domesticated	Domesticated	Domesticated	Domesticated		Domesticated	domesticated																		Domesticated	Intraspecific	Domesticated	Domesticated	Domesticated	Intraspecific	Intraspecific	Intraspecific	Interspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intergeneric or Higher	Intergeneric or Higher	Intergeneric or Higher	Domesticated	Domesticated	Domesticated	Intraspecific	Intraspecific	Domesticated	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Intraspecific	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Domesticated	Intergeneric or Higher	Intergeneric or Higher	Domesticated	Domesticated	Domesticated	Domesticated	Intraspecific	Domesticated	Intergeneric or Higher	Domesticated	Experimental Evolution	Intraspecific	Domesticated	Domesticated	Intraspecific
39	Empirical Evidence	Linkage Mapping	Association Mapping	Linkage Mapping	Linkage Mapping	Candidate Gene	Candidate Gene	Candidate gene	Candidate gene	Linkage Mapping			Linkage mapping	candidate gene	Candidate Gene	Candidate gene	Candidate gene	Candidate gene	Candidate gene		candidate gene	Linkage mapping																		Linkage Mapping	Linkage Mapping	Linkage Mapping	Candidate Gene	Candidate Gene	Linkage Mapping	Candidate Gene	Linkage Mapping	Linkage Mapping	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene &2 Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Association Mapping	Association Mapping	Linkage Mapping	Linkage Mapping &2 Linkage Mapping	Linkage Mapping	Candidate Gene	Candidate Gene	Linkage Mapping	Association Mapping	Linkage Mapping	Linkage Mapping	Candidate Gene	Candidate Gene	Candidate Gene	Candidate Gene	Linkage Mapping	Candidate Gene	Candidate Gene	Linkage Mapping	Candidate Gene	Linkage Mapping	Candidate Gene	Candidate Gene	Linkage Mapping	Linkage Mapping	Candidate Gene	Candidate Gene	Linkage Mapping	Linkage Mapping	Candidate Gene	Linkage Mapping	Association Mapping	Linkage Mapping	Association Mapping	Linkage Mapping	Candidate Gene
40	Molecular Details	800 bp TE insertion; probably disrupts the last 61 amino acids of the SBEI protein	Excision of the full-length FERV1 elevement leaving the two LTR residues	insertion of transposable element in an exon	insertion of transposable element Ac within a large intron; affecting transcripts. The five transcripts found in P-RR plants are absent in P-VV. A chimeric transcript containing part of Ac sequence is found.	two non‐conservative mutations, one leads to an amino acid substitution and the other to a frame shift resulting in a smaller protein	Insertion in gene Y, in the second intron. Transposon cis includes 4 genes.	Insertion of a 7,764 bp non-autnomous retrotransposon RIRE_X in the 9th exon of the wx gene, which is absent in most glutinous rice species (which have a 23bp duplication in exon 2).	an insertion of miniature inverted-repeat transposable element (MITE) called ahMITE1 causes a frameshift, resulting in a putatively truncated protein sequence	insertion of a Helitron transposon of 4320 bp starting with 5' TC and ending with 3'CTAG containing a 17 bp palindromic region forming a hairpin - prevents transcription	two copies of Tip100 inserted in the CHS‐D intron	11.5 kbp TE insertion (Helitron Ipomoea tricolor one, Hel-lt1) within DFR-B gene exon 5; affecting anthocyanins biosynthesis.Insertion with 5'-TC and CTAG-3' at its termini; integrated between 5'-A and T-3' within the 437-bp mobile element-likesequence MELS2 in intron 5 of the DFR-Bgene. Orientation of the insertion opposite of DFR-B gene.	Insertion of a Dasheng retrotransposon 12 bp upstream of the ATG codon of the OsCHI gene, affecting flavonoïd metabolism		8 kb segment of unrelated DNA inserted into the coding sequence of the Chinese Spring(Triticum aestivum) gene but absent from its counterpart in Cheyenne(Aegilops tauschii).	Retrotransposon SORE-1 is inserted at nucleotide 692 from the start codon in exon 1 of the GmphyA2 gene. The element comprised two 383-bp long terminal repeats (LTRs) and an internal domain of 5,472 bp.	Insertion of Tpn-botan, a Tpn1-related-element in the 2nd intron of the DP gene, followed by a delition of exons 3 to 9 and most part of the TE itself.	Ac/Ds transposition (from maize lines containing Ac site) and PCR study of the fusion in P1 gene	Ac/Ds transposition (from maize lines containing Ac site) and PCR study of the fusion in P1 gene		Dissociation (DS) transposable element (409 bp) excisition in exon sequence of the waxy (wx) locus for wx-m1 giving S5 and S9		an increased level of APO1 expression in apo1-D alleles was caused by the insertion of nDart1-0 in the APO1 promoter. This suggests that a cis-element(s) involved in the negative regulation of APO1 expression might exist in the 3.5kb upstream region of APO1.																	577-bp insertion of a transposable element named AcWHITE in the 5′ upstream region of the white allele of B2. A 8-bp target site duplication (GTTATA AC) and a 7-bp terminal inverted repeat (CAAGGTT) were identified at both ends of this insertion - no SNP detected in the coding region	insertion of a transposon Tntransib (2581 bp) in ABCA2 which changes splicing sites in the transcript and lead to an indel in the coding region: change of 1551VETLAHALGFLRHLDKR1567 into 1551AHWGK- LYGSNTQN1563	insertion of a 5.5-kb LTR retrotransposon Renovator upstream of the gene (256‐bp upstream of the predicted start codon for NBSt2K59; in the same orientation as the gene)	insertion of a 4.2 kb non-LTR retrotransposon in the promoter (672 bp upstream of the start codon of CaAn2) which may activate expression of CaAn2 by recruiting transcription factors at the 3' UTR	7524 bp insertion at the 5'end of CYP19A1 of an intact endogenous retrovirus (99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains suggesting a recent integration) - The ERV 3'LTR contains a powerful transcriptional enhancer and core promoter with TATA box.	insertion of a copia retrotransposon within the gene Rhg1 Glyma.18G022500 (α-SNAP-encoding). This transposable element is intact and resides within intron 1; anti-sense to the rhg1-a α-SNAP open reading frame.	5′688–bp insertion of a transposon of the LTR-Gypsy family which generates a new splice donor site (gt) 42 bases upstream of the wild-type donor site; thus generating a 14–amino acid deletion in the corresponding transcript	The mutant phenotype is caused by a dramatic decrease of zic1/zic4 expression in the dorsal somites. The insertion of a transposon (“Albatross”) into an enhancer region (downstream of zic4) of the transcription factors zic1 and zic4 causes this phenotype. Both genes are expressed by a bi-directional promoter. The transposon insertion is proposed to interfere with the transcriptional regulation of zic1/zic4; resulting in the disturbance of the expression of the transcription factors in the dorsal somites (the expression of zic1/zic4 in other parts of the body is not affected in this mutant) and ultimately causing a ventralized trunk phenotype. In Inoue et al. (2017) it was shown that the transposon “Albatross” is actually larger than originally predicted; and is now called “Teratorn”. Teratorn is around 180kb long and appears to originate from the fusion of a DNA transposon and a herpesvirus.	insertion of a partial 481 bp fragment related to a transposable element of the helitron class - maybe other causing mutations as well at this ebony locus (including one fixed amino acid change whose phenotypic effect has not been investigated) - increased expression associated with lighter pigmentation	insertion of a Juan transposable element in the regulatory sequence. The insertion is almost fixed in the Rhône Valley but barely present in Mayotte - mutation associated with increased expression of the gene	insertion of a Doc transposable element around 200 bp upstream of the putative transcription start site - mutation associated with increased expression of the gene	A non-autonomous 1383bp P-element is inserted 97bp upstream of the Hsp70Ba transcription start site. The P-element intervenes between the second and third heat shock response elements (HSEs).	Insertion of a 1222bp non-autonomous P-element at position -184 relative to the Hsp70Ba transcription start site. The P-element intervenes between the second and third heat shock response elements (HSEs).	A 1447 bp fragment corresponding to the 39 end of a jockey element is inserted 107 bps upstream of the hsp70Ba transcription start site in the T strain. The insertion intervenes between HSEs 2 and 3; displacing HSEs 3 and 4 as well as three GAGA elements.	insertion of the transposable element B104/roo in the exon 3 of the Phenylalanine hydroxylase gene. Its presence alters the Phenylalanine hydroxylase splicing pattern; producing at least two aberrant mRNAs which contain part of the B104 sequence interrupting the coding region. This aberrant splicing is provoked by the use of a cryptic donor site encoded by the B104 3' long terminal repeat in combination with either the gene intron 3 acceptor site or a novel acceptor site generated by the target duplication caused by transposition. One of them; referred as mRNA type 1; encodes a truncated protein that could be predictably non-functional. In mRNA type 2; in spite of a 42 nt insertion; the Phenylalanine hydroxylase reading frame is not altered and it would encode for a protein with 14 extra amino acids which would be able to account for the low enzyme activity detected in this mutant.	insertion of a 8kb blood retrotransposon in the 3' region of the Gpdh gene 66bp downstream of the stop codon. This mutation induces a GPDH isozyme-GPDH-4-and alters the pattern of expression of the three normal isozymes-GPDH-1 to GPDH-3.	Insertion of a 0.68kb truncated P-element 47bp downstream of the transcription start site.	A locus containing three genes (dsx; Nach-like and UXT) displays dimorphic sequences strictly associated with the mimetic/nonmimetic phenotypes. Expression of dox; UXT but not Nach-like showed differences correlated with phenotype in female hind wings.	y[2-717] - Inversion that occurred between two hobo elements: one located 129 bp from the start site of yellow transcription and the other in the distal telomere region. The yellow phenotype is caused by the separation of the body and wing enhancers from the transcription unit.	insertion of a CHR-2 SINE retroposon in exon 2 of MMP20 which would result in premature truncation of the MMP20 protein owing to stop codons in all possible reading frames of the CHR-2 SINE. The length of the MMP20 SINE ranges from 302 bp (B. musculus) to 318 bp (B. physalus). This mutation is found in eight investigated species of baleen whales. Other inactivating mutations (nonsense and frameshift mutations) are found in various species	premature stop codon in exon 7 (Lys295Ter) and deletion leading to the loss of six of its nine exons &2 deletion leading to the loss of six of its nine exons - the high abundance of repetitive elements in the CTSE region (more than 3.8 interspersed elements per kilobase as compared with 2 for the genome average) might have contributed to the deletion of six out of the nine exons of CTSE by nonallelic homologous recombination between these repetitive elements - the CTSE gene has been disrupted by the insertion of long interspersed elements (LINEs) and short interspersed elements (SINEs) in exons 7 and 9; disrupting the protein coding region - Exon 9 was disrupted by the insertion of a LINE2 Plat1m element which was further disrupted by the insertion of a SINE Mon1f3 element	3-4 copies of the amylase gene; which coincides with increased levels of amylase activity in saliva	Copy Number Variation	Copy Number Variation	Copy Number Variation	Trans_3538426_3538832 – insertion of a transposable element = a cut and paste DNA transposon Tc5B - which is part of the TcMar-Tc4 transposon superfamily– 406bp of the reference sequence seem to be disrupted- Steffen Hahnel comment : Since we didn't re-amplify the insertion by PCR; we don't know its exact location; sequence and size. Its identification is only based on the illumina reads of genome sequencing of JU3125.	insertion of a transposable element Bari-Jheh associated with downregulation of Juvenile hormone epoxy hydroxylase 2 (Jheh2) and Jheh3 in nonstress conditions and with upregulation of Jheh1 and Jheh2 and downregulation of Jheh3 under oxidative stress conditions	insertion of a Rider transposable element within the coding region	insertion of a transposable element island (13 TE interspersed by simple repeats) of approximately 30 kb; located 1862 bp upstream of Zmr1 start codon - analysis of knock out lines of the TE island insertion &2 several candidate SNP - tests using reporter transgenes	insertion of an LTR-retrotransposon (5832-bp) in the 11th intron resulting after splicing in an additional 397-bp fragment constituted of 3 new exons inserted between exons 11 and 12. Generates truncated protein with two stop codons	2 insertions of Tip100 in opposite orientation at different sites within the same intron	insertion of a 3.9kb long transposable element Tip100 in intron	partial 1.5kb Accord element ; possibly a driver of nicotine-sensitive expression ; the resistant strain also has a gene tandem duplication (CNV) that may play complementary role in resistance levels	insertion of a 186bp POGON1 element in the 3'UTR	A 2.5 kb retrotransposon in exon 2 severely truncates the protein	Complex Haplotype in first intron perfectly associated with phenotype: 173 fixed single-nucleotide polymorphisms (SNPs) in complete linkage disequilibrium (LD) located 23	2.4kb deletion (intron 1)	Transposon insertion TS1-9 (Exon 10)	Transposon insertion TS1-7 (Exon 3)	Transposon insertion TSI-10 (Intron 12)	Transposon insertion TSI-2 (intron 1)	Transposon insertion TSI-11 (Intron 12)	Gret1 retrotransposon deletion; leaving behind its 3'-LTR flanked by 5 bp of a duplicated target site	Gret1 insertion polymorphism + R188S + Q213P	Gret1 retrotransposon insertion	unknown ; observed transposon insertion in intron and promoter variation	LINE-mediated retrotransposition of the CyclophilinA gene into 3'UTR (exon 8) of TRIM5alpha	LINE-mediated retrotransposition of the CyclophilinA gene between exons 7 and 8 of TRIM5alpha	Gene duplication	insertion of the transposable element Dissociation	TE (Tcs1) insertion triggering cold-dependent expression	TE (Tcs2) insertion triggering cold-dependent expression	Deletion	insertion of transposable element Ac	Acquisition of enhancer activity in transposons via several base-pair substitutions	insertion of a non-autonomous rbg transposable element in the untranslated leader sequence of the O2 gene	Ty retrotranposition resulting in a coding frameshift	Truncated protein due to insertion of a transposable element. Reversion to resistance among descendants of mutant X75 was associated with excision of the newly transposable element Ac.	full-length (7125 bp) FERV1 endogenous retrovirus insertion in intron	256-bp transposable element insertion in exon 4	Insertion of a LTR retrotransposon
41	Insertion Size (in bp)						23018	7764		4320	about 3900*2	11468	7300		8200	6238	1227				409		Unknown																	577	2581	5500	4200	7524		5688		481
42	TE Class						II	I	II	II	II	II	I		I	I	II	Ac	Ac		Ds		Unknown																			I	I	I	I	I		II
43	TE Order						TIR	LTR	TIR	helitron	TIR	Helitron	LTR		LTR	LTR	TIR						Unknown																			LTR retrotransposon		retrovirus	LTR retrotransposon	Gypsy		Helitron
44	TE Superfamily						CACTA			Helitron	hAT					Copia-like		hAT	hAT		Unknown		Unknown																						copia		Albatros	Helitron
45	Molecular Type	Coding	Cis-regulatory	Coding	Cis-regulatory	Coding	Cis-regulatory	Coding	Coding	Cis-regulatory (intron 2)	Coding (Exon) and Cis-regulatory (Intron)	Coding	Cis-regulatory		Other	Coding	Coding	Cis-regulation	Cis-regulation		Cis-regulatory		Cis-regulatory																	Cis-regulatory	Coding	Cis-regulatory	Cis-regulatory	Cis-regulatory	Cis-regulatory	Coding	Cis-regulatory	Cis-regulatory	Cis-regulatory	Cis-regulatory	Cis-regulatory	Cis-regulatory	Cis-regulatory	Coding	Cis-regulatory	Coding	Unknown	Cis-regulatory	Coding	Coding &2 Coding	Gene Amplification	Gene Amplification	Gene Amplification	Gene Amplification	Coding	Cis-regulatory	Coding	Cis-regulatory &2 Cis-regulatory	Coding	Unknown	Unknown	Cis-regulatory	Cis-regulatory	Coding	Cis-regulatory	Cis-regulatory	Coding	Coding	Cis-regulatory	Cis-regulatory	Cis-regulatory	Cis-regulatory	Unknown	Cis-regulatory	Cis-regulatory	Other	Other	Gene Amplification	Cis-regulatory	Cis-regulatory	Cis-regulatory	Gene Loss	Unknown	Cis-regulatory	Cis-regulatory	Coding	Coding	Cis-regulatory	Coding	Coding
46	Presumptive Null	Yes	No	Yes	No	Yes	No	Yes	No	Yes		Yes	Yes		Yes	No	Yes	No	No		No		No																	Yes	Yes	No	No	No	No	Unknown	No	No	No	No	No	No	No	No	No	No	No	No	Yes	Yes &2 Yes	No	No	No	No	Yes	No	Yes	No &2 No	Yes	No	No	Unknown	No	Yes	No	No	Yes	Yes	No	No	No	No	Unknown	No	Unknown	No	No	No	No	No	No	Yes	No	No	No	Yes	Yes	No	Yes	Yes
47	SNP Coding Change																																																											Nonsense &2								&2
48	Codon-Taxon-A																																																											&2								&2
49	Codon-Position																																																											&2								&2
50	Codon-TaxonB																																																											&2								&2
51	AminoAcid-Taxon A																																																											Lys &2								&2
52	AA-Position																																																											295 &2								&2
53	AminoAcid-Taxon B																																																											STP &2								&2
54	Aberration Type	Insertion	Deletion	Insertion	Insertion	Substitution + Délétion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion		Insertion	Insertion	Insertion+Delition	Fusion, exon shuffling	Fusion, exon shuffling		insersion + subsequent excisition	Insertion	Insertion																	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Unknown	Inversion	Insertion	SNP &2 Deletion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion &2 SNP	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion	Unknown	Deletion	Insertion	Insertion	Insertion	Insertion	Insertion	Deletion	Unknown	Insertion	Unknown	Insertion	Insertion	Complex Change	Insertion	Insertion	Insertion	Complex Change	Insertion	SNP	Insertion	Insertion	Insertion	Insertion	Insertion	Insertion
55	Aberration Size	100-999 bp	1-10 kb	1-10 kb	1-10 kb		10-100 kb	1 - 10 kb	205 bp	1-10 kb	1-10 kb	11.5 kbp	7.3kbp		1-10 kb	1-10 kb	1-10kb	around 60 kb	around 60 kb		9 & 6 pb	1-10kb	Unknown																	100-999 bp	1-10 kb	1-10 kb	1-10 kb	1-10 kb	1-10 kb	1-10 kb	100-1000 kb	100-999 bp	1-10 kb	1-10 kb	1-10 kb	1-10 kb	1-10 kb	1-10 kb	1-10 kb	100-999 bp		100-1000 kb	100-999 bp	&2	1-10 kb	1-10 kb	1-10 kb	1-10 kb		1-10 kb		10-100 kb &2	100-999 bp	1-10 kb	1-10 kb	1-10 kb	100-999 bp	1-10 kb		1-10 kb	1-10 kb	1-10 kb	1-10 kb	1-10 kb	1-10 kb	1-10 kb		1-10 kb		1-10 kb	1-10 kb		1-10 kb	1-10 kb	1-10 kb		1-10 kb		1-10 kb	1-10 kb	unknown	1-10 kb	100-999 bp	1-10 kb
56	Comments	@TE; the insertion eliminates a large transcript and increases the production of a short transcript. The transmembrane protein interacts and increases ALDH-III activity which metabolizes benzaldehyde and increase resistance to carbofuran. But the resistance is also affected by the genetic background	Only one genome of capuchin was investigated - @ParallelEvolution in mice; humans; dogs; rats @TE	@TE The transposable element insertion acts on the regulation of the three neighboring genes Jheh1 Jheh2 and Jheh3 - http://flybase.org/reports/FBal0243312 - http://flybase.org/reports/FBal0243313	@TE	Modifier l'entrée 1195 dans GePheBase afin d'ajouter la substitution en plus de l'indel déjà indiquée	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE		@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE Cluster of paralogous transcription factors https://omia.org/OMIA000201/9913/	A second study (Falchi et al. 2014) showed an association between copy number of Amy gene and obesity - Multiple rounds of gene duplications - The gene duplications likely postdated the human Neanderthal split (Inchley et al. 2016) @TE	CNV among dog breeds; with no amplification in Arctic and Australian breeds @ParallelEvolution in humans; mice; rats boars @TE	@TE	@TE	@TE - http://flybase.org/reports/FBal0190391	@TE	@TE	@TE @SuccessiveMutations @SelectiveSweep - http://flybase.org/reports/FBal0014805	@TE	@TE	@TE reporter constructs	@TE Parallelism: repeated loss-of-function	@TE Parallelism: repeated loss-of-function	@TE Parallelism: repeated loss-of-function	@TE Parallelism: repeated loss-of-function	@TE Parallelism: repeated loss-of-function	@TE Parallelism: repeated loss-of-function	@TE Parallelism: repeated loss-of-function	@TE	@Pleiotropy @TE; Affects a conserved melanocyte enhancer	@Pleiotropy @TE; Affects a conserved melanocyte enhancer	@TE	@TE	@TE	@TE	@TE; WormBase ID: WBGene00004041	@TE @Epistasis	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE @ChimericGene	@ChimericGene @TE; Trim5CypA2 clearly has restriction activity because it can block infection by HIV-2 simian immunodeficiency virus (SIV)AGMtan and feline immunodeficiency virus (FIV). This difference in restriction properties results from a point mutation leading to an H69R change in the CypA domain	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE	@TE ; Mimicry ; @Fitness Adaptive ; Linkage + Association Mapping	@TE; both taxa are hemizygous for the supergene S	The QTL harbors a pair of cytochrome P450 genes. According to gene expression Cyp28d1 is the best candidate but Cyp28d2 is also possible. @TE described with nicotine-dependent effect on gene expression in the follow-up article by Chakraborty et al.: Intergenic element between a gene copy is the 5′ end of Accord; a long terminal repeat (LTR) retrotransposon.; Insertion of Accord upstream of another gene called Cyp6g1 has been linked to upregulation of the encoded cytochrome P450 enzyme suggesting that the retrotransposon may be responsible for the upregulated expression of the Cyp28d gene	@TE; coding or regulatory mutation	this allele with 2 @TE is supposed to derive from an allele with 1 TE. coding or regulatory mutation	@TE; possible null mutation	@TE ; check for UniProtKB and orthology with Cmr1	@TE	9–13 diploid copies of the amylase gene in brown rats and 6–7 copies in black rats and wood rats @ParallelEvolution in humans; dogs; rats boars @TE	@ParallelEvolution in mice; humans; dogs; rats boars @TE	@ParallelEvolution in mice; humans; dogs; rats @TE	@TE lack of acid secretion in the platypus stomach - this is a characteristic feature of monotremes whose gastric juice is above pH 6	@TE @ParallelEvolution in Kogia whales. Cladistic analyses suggest that functional teeth were lost in the common ancestor of crown-group Mysticeti.	@TE hobo element http://flybase.org/reports/FBal0104919
57	User Feedback												https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.13021
58													.
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100