| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | Order | Lineage | Superorder | Orders Scientific Name (inferred >50 MYA divergence times) | Family Scientific Name | Orders English Name | MYA div closest ordinal relative | # species/order | # species/order planned | Scientific Name | English Name | NCBI taxon ID | Status | Assembly ID | Assembly ID main haplotype | Accession # for main haplotype | RefSeq annotation main haplotype | UCSC Browser main haplotype | Sex chromosomes main haploptype | Assembly IDs other high-quality haplotypes | Accession #s other high-quality haplotypes | Assembly IDs alternate haplotypes | Accession #s alternate haplotypes | Mitochondria high-quality assembly | Annotation status | SRA VGP transcriptome | SRA other transcriptome | Assembly tech | # contigs | v | Assembly Size | QV | sex | Progress notes | IUCN (2016-2024) | CITES | Main project | Second project | Primary contact | Other contacts | Primary Funding | Initial Publication | ||
2 | m1 | Mammals | Afrotheria | Proboscidea | Elephantidae | Elephants | 62.97 | 3 | 2 | Elephas maximus indicus | Asian elephant | 99487 | 4 | mEleMax1 | mEleMax1.hap1 | GCA_051911825.1 | GCF_024166365.1 | GCA_051911825.1 | Has X and Y | mEleMax1.hap2 | GCA_051911805.1 | CM123153.1 | Completed NCBI | PRJNA844231 | HiFi, Hifiasm Hi-C phasing | 186 | 103 | 3,377,912,597 | M | Updated phased assembly since data freeze v1 | Endangered | VGP | colossal | Camila Mazzoni <mazzoni@izw-berlin.de> | Ben Lamm <ben@colossal.com> | University of Turku, Colossal | ||||||||
3 | m1 | Mammals | Afrotheria | Proboscidea | Elephantidae | Elephants | 62.97 | Loxodonta africana | African elephant | 9785 | mLoxAfr1 | mLoxAfr1.hap2 | GCA_030014295.1 | GCF_030014295.1 | GCF_030014295.1 | Has X and Y | mLoxAfr1.hap1 | GCA_030020305.1 | CM057448.1 | Completed NCBI | SRX16844417;SRX16844418;SRX16844419;SRX16844640;SRX16844641;SRX16844642;SRX16872535;SRX16872536;SRX16872537;SRX16872783 | HiFi, Hifiasm Hi-C phasing | 1,111 | 880 | 3,540,893,228 | M | Endangered | VGP | Colossal | Ben Lamm <ben@colossal.com> | Erich Jarvis <ejarvis@rockefeller.edu> | Colossal | ||||||||||||
4 | m2 | Mammals | Afrotheria | Hyracoidea | Procaviidae | Hyraxes | 62.97 | 4 | 1 | Heterohyrax brucei | yellow-spotted rock hyrax | 77598 | 4 | mHetBru1 | mHetBru1.pri | GCA_028571685.1 | GCA_028571685.1 | Has X and Y | mHetBru1.alt | GCA_028571665.1 | Wait | HiFi, Hifiasm solo | 338 | 62 | 3,488,059,404 | M | Least Concern | VGP | Gene Myers <gene@mpi-cbg.de> | Camila Mazzoni <mazzoni@izw-berlin.de> | Max Planck Society | |||||||||||||
5 | m3 | Mammals | Afrotheria | Sirenia | Dugongidae | Dugongs | 64 | 4 | 2 | Dugong dugon | dugong | 29137 | 4 | mDugDug1 | mDugDug1.hap1 | GCA_030035585.1 | GCA_030035585.1 | Has X only | mDugDug1.hap2 | GCA_030020955.1 | Wait | HiFi, Hifiasm Hi-C phasing | 198 | 294 | 3,158,488,110 | F | Endangered | VGP | Beth Shapiro <bashapiro@ucsc.edu> | Federica DiPalma <Federica.Di-Palma@earlham.ac.uk> | Beth Shapiro and Federica DiPalma | |||||||||||||
6 | m3 | Mammals | Afrotheria | Sirenia | Trichechidae | Manetees | 64 | Trichechus inunguis | Amazon manatee | 9777 | mTriInu1 | mTriInu1.hap2 | GCA_046562895.1 | GCA_046562895.1 | Has X and Y | mTriInu1.hap1 | GCA_046562985.1 | HiFi, Hifiasm Hi-C phasing | 695 | 401 | 3,320,339,069 | M | Vulnerable | Amazoomics : Genomics of Brazilian Biodiversity | Alexandre Aleixo <alexandre.aleixo@itv.org> | Sibelle Vilaca <sibelle.vilaca@itv.org> | Vale | |||||||||||||||||
7 | m4 | Mammals | Afrotheria | Macroscelidea | Macroscelididae | Elephant shrews | 75 | 17 | 1 | Rhynchocyon petersi | black and rufous elephant shrew | 320637 | 4 | mRhyPet1 | mRhyPet1.hap1 | GCA_043290085.1 | GCA_043290085.1 | Has X and Y | mRhyPet1.hap2 | GCA_043290065.1 | CM091805.1 | Ready* Nov 23 2024 | HiFi, Hifiasm Hi-C phasing | 1,238 | 468 | 5,620,354,054 | M | Least Concern | VGP | Erich Jarvis <ejarvis@rockefeller.edu> | Susie Bartlett <sbartlett@wcs.org> | HHMI | ||||||||||||
8 | m5 | Mammals | Afrotheria | Tenrecidae | Oryzorictinae | Tenrecs | 64 | 30 | 1 | Tenrec ecaudatus | tailless tenrec | 94439 | 4 | mTenEca1 | mTenEca1.hap1 | GCA_050624435.1 | GCF_050624435.1 | Has X and Y | mTenEca1.hap2 | GCA_050624465.1 | Completed NCBI | PRJNA1270731 | HiFi, Hifiasm Hi-C phasing | 2,355 | 2,180 | 3,922,859,826 | M | Least Concern | VGP | Erich Jarvis <ejarvis@rockefeller.edu> | Ryan Langlois<langlois@umn.edu> | HHMI | ||||||||||||
9 | m6 | Mammals | Afrotheria | Afrosoricida | Chrysochloridae | Golden moles | 64 | 21 | 1 | Amblysomus hottentotus | hottentot golden mole | 9391 | 3 | Adam Ferguson sent samples to RU Nov 22 2024. Kim AfricaBP fresh frozen Sep10 2024; Jarvis Funding; Adam Fergsuson. AfricaBP Ntanga cells in DMSO Jan 14, 2024 (Will try again on cell lines Acclaim Feb 9, 2024) too many passages, not enough data for Pacbio sequencing (Silke Arnt); Auroa contact with Camila | Least Concern | VGP | Erich Jarvis <ejarvis@rockefeller.edu> | Adam Ferguson<aferguson@fieldmuseum.org> | HHMI | |||||||||||||||||||||||||
10 | m7 | Mammals | Afrotheria | Tubulidentata | Orycteropodidae | Aardvark | 76 | 1 | 1 | Orycteropus afer | aardvark | 9818 | 3 | mOryAfe1 | SRX4745740 | In curation at RU Aug 2025. Pause until SPRQ HiFi upgrade Jan 2025 Bronx Zoo sample. More Pacbio Shearing Oct 8, 2024. Hi-C is complete. Might not be enough for PacBio, but library is being sequenced Sep 11 2024. Kim AfricaBP fresh frozen Sep10 2024; Another sample Hi-C complete = 10x Pacbio coverage thus far Aug 15 2024. Started at RU Jan 25, 2024. Pacbio May 2024; Sample from Bronx Zoo obtained Dec 14, 2023; lost original samples in shipment to MPI | Least Concern | VGP | Erich Jarvis <ejarvis@rockefeller.edu> | HHMI | ||||||||||||||||||||||||
11 | m8 | Mammals | Xenarthra | Pilosa (Vermilingua) | Myrmecophagidae | Anteaters | 55 | 4 | 1 | Tamandua tetradactyla | Southern tamandua | 48850 | 4 | mTamTet1 | mTamTet1.pri | GCA_023851605.1 | GCA_023851605.1 | Has X and Y | mTamTet1.alt | GCA_023853755.1 | CM043432.1 | Wait? | CLR I, FALCON unzip | 1,162 | 201 | 3,205,741,135 | M | Least Concern | VGP | Camila Mazzoni <mazzoni@izw-berlin.de> | Marcela Uliano-Silva <mu2@sanger.ac.uk> | Max Planck Society | ||||||||||||
12 | m9 | Mammals | Xenarthra | Pilosa (Folivora) | Megalonychidae | Sloths | 55 | 6 | 1 | Choloepus didactylus | Linnaeus's two-toed sloth | 27675 | 4 | mChoDid1 | mChoDid1.pri | GCA_015220235.1 | GCF_015220235.1 | GCF_015220235.1 | Has X and Y | mChoDid1.alt | GCA_015220265.1 | AY960980.1 | Completed NCBI | PRJNA516733 two different data sets named differently | SRX6800432;SRX6800433;SRX6800434;SRX6800435;SRX8148218;SRX8148219;SRX8148220;SRX8148221;SRX8148222;SRX8148223 | CLR I, FALCON unzip | 1,385 | 146 | 3,214,702,648 | M | Least Concern | VGP | Camila Mazzoni <mazzoni@izw-berlin.de> | Marcela Uliano-Silva <mu2@sanger.ac.uk> | Marie Skłodowska-Curie Fellowship, Max Planck Society | |||||||||
13 | m10 | Mammals | Xenarthra | Cingulata | Dasypodidae | Armadillos | 67 | 21 | 1 | Dasypus novemcinctus | nine-banded armadillo | 9361 | 4 | mDasNov1 | mDasNov1.1.hap2 | GCA_030445035.2 | GCF_030445035.2 | GCF_030445035.2 | Has X and Y | mDasNov1.hap1 | GCA_030445055.2 | Completed NCBI | SRA SRR24630298 | SRX7355008;SRX7355009;SRX7355010;SRX7355011;SRX7355012;SRX7355013;SRX7355014;SRX7355015;SRX7355016;SRX7355017 | HiFi, Hifiasm Hi-C phasing | 1,310 | 539 | 3,570,966,115 | M | Least Concern | VGP | BRAIN | Ed Lein <edl@alleninstitute.org> | Erich Jarvis <ejarvis@rockefeller.edu> | Allen Institute | |||||||||
14 | m11 | Mammals | Supraprimates (Euarchontoglires) | Primates (Catarrhines) | Hominidae | Apes & Old World monkeys | 30 | 160 | 10 | Homo sapiens | human | 9606 | 5 | T2T-CHM13v2.0 | T2T-CHM13v2 | GCA_009914755.4 | GCF_009914755.1 | GCA_009914755.4 | Has X and Y | mHomSap3.pat, mHomSap3.mat, GRCh38.p14 | GCA_016700455.2, GCA_016695395.2, GCF_000001405.40 | Completed NCBI | HiFi, ONT, Verkko | 24 | 24 | 3,117,275,501 | M | mHomSap3 being done over with HiFi and ONT for T2T genome. | Least Concern | VGP | HPRC | Adam Phillippy <adam.phillippy@nih.gov> | Erich Jarvis <ejarvis@rockefeller.edu> | NIH | PMID: 35357919 | |||||||||
15 | m11 | Mammals | Supraprimates (Euarchontoglires) | Primates (Catarrhines) | Hominidae | Apes & Old World monkeys | 30 | Pan troglodytes | chimpanzee | 9598 | mPanTro3 | mPanTro3.hap1 | GCA_028858775.2 | GCF_028858775.2 | GCF_028858775.2 | Has X and Y | mPanTro3.hap2 | GCA_028858805.2 | D38113.1 | Completed NCBI | SRX20102265;SRX20102266;SRX20102267;SRX20102268;SRX20102269;SRX20102270;SRX20102271;SRX20102272;SRX20102273;SRX20102274 | HiFi, ONT, Verkko + Hi-C phasing | 26 | 26 | 3,177,756,316 | M | Endangered | T2T | Evan Eichler <ee3@uw.edu> | Adam Phillippy <adam.phillippy@nih.gov> | NIH | PMID: 39131277 | ||||||||||||
16 | m11 | Mammals | Supraprimates (Euarchontoglires) | Primates (Catarrhines) | Hominidae | Apes & Old World monkeys | 30 | Pan paniscus | bonobo | 9597 | mPanPan1 | mPanPan1.pri | GCA_029289425.3 | GCF_029289425.2 | GCA_029289425.3 | Has X and Y | mPanPan1.alt | CM055497.2 | Completed NCBI | ERX6700457;SRX18280098;SRX18797586;SRX18797587 | HiFi, ONT, Verkko trio | 37 | 31 | 3,244,905,271 | M | Make a new assemby combo, by moving the Y from mPanPan1.pat into mPanPan1.mat. | Endangered | T2T | Evan Eichler <ee3@uw.edu> | Adam Phillippy <adam.phillippy@nih.gov> | NIH | PMID: 39131277 | ||||||||||||
17 | m11 | Mammals | Supraprimates (Euarchontoglires) | Primates (Catarrhines) | Hominidae | Apes & Old World monkeys | 30 | Gorilla gorilla | gorilla | 9593 | mGorGor1 | mGorGor1.pri | GCA_029281585.3 | GCF_029281585.2 | GCA_029281585.3 | Has X and Y | mGorGor1.alt | CM082747.1 | Completed NCBI | ERX11571544;ERX11571572;ERX11571582;ERX11571586;ERX11571587 | HiFi, ONT, Verkko trio | 26 | 26 | 3,545,850,631 | M | Will have to remove Y from pat during the alignment, because already in mat | Critically Endangered | T2T | Evan Eichler <ee3@uw.edu> | Adam Phillippy <adam.phillippy@nih.gov> | NIH | PMID: 39131277 | ||||||||||||
18 | m11 | Mammals | Supraprimates (Euarchontoglires) | Primates (Catarrhines) | Hominidae | Apes & Old World monkeys | 30 | Pongo abelii | Sumatran orangutan | 9601 | mPonAbe1 | mPonAbe1.hap1 | GCA_028885655.2 | GCF_028885655.2 | GCF_028885655.2 | Has X and Y | mPonAbe1.hap2 | GCA_028885685.2 | X97707.1 | Completed NCBI | HiFi, ONT, Verkko trio | 41 | 30 | 3,259,870,029 | M | Critically Endangered | T2T | Evan Eichler <ee3@uw.edu> | Adam Phillippy <adam.phillippy@nih.gov> | NIH | PMID: 39131277 | |||||||||||||
19 | m11 | Mammals | Supraprimates (Euarchontoglires) | Primates (Catarrhines) | Hominidae | Apes & Old World monkeys | 30 | Pongo pygmaeus | Bornean orangutan | 9600 | mPonPyg2 | mPonPyg2.hap1 | GCA_028885625.2 | GCF_028885625.2 | GCF_028885625.2 | Has X and Y | mPonPyg2.hap2 | GCA_028885525.2 | D38115.1 | Completed NCBI | SRX13828949;SRX13828951;SRX13828952;SRX13828953;SRX13828954;SRX13828955;SRX13828956;SRX13828957;SRX13828958;SRX13828959 | HiFi, ONT, Verkko + Hi-C phasing | 26 | 26 | 3,220,951,552 | M | Critically Endangered | T2T | Evan Eichler <ee3@uw.edu> | Adam Phillippy <adam.phillippy@nih.gov> | NIH | PMID: 39131277 | ||||||||||||
20 | m11 | Mammals | Supraprimates (Euarchontoglires) | Primates (Catarrhines) | Hylobatidae | Apes & Old World monkeys | 30 | Symphalangus syndactylus | siamang gibbon | 9590 | mSymSyn1 | mSymSyn1.hap1 | GCA_028878055.3 | GCF_028878055.3 | GCF_028878055.3 | Has X and Y | mSymSyn1.hap2 | GCA_028878085.3 | AB504750.1 | Completed NCBI | SRX5506079;SRX5506080 | HiFi, ONT, Verkko + Hi-C phasing | 27 | 27 | 3,262,904,224 | M | Endangered | T2T | Evan Eichler <ee3@uw.edu> | Adam Phillippy <adam.phillippy@nih.gov> | NIH | PMID: 39131277 | ||||||||||||
21 | m11 | Mammals | Supraprimates (Euarchontoglires) | Primates (Catarrhines) | Cercopithecidae | Apes & Old World monkeys | 30 | Macaca fascicularis | crab-eating macaque | 9541 | T2T-MFA8v1.0 | mMacFas1.hap1 | GCA_037993035.1 | GCF_037993035.1 | GCF_037993035.1 | Has X only | Completed NCBI | Verkko HiFi + ONT | 21 | 21 | 3,042,914,375 | F | Parthenogenic cell line, only haploid. Contact Guojie for permission | Endangered | T2T | Evan Eichler <ee3@uw.edu> | Yafei Mao <yafmao@sjtu.edu.cn> | National Natural Science Foundation of China | PMID: 40011769 | |||||||||||||||
22 | m11 | Mammals | Supraprimates (Euarchontoglires) | Primates (Catarrhines) | Cercopithecidae | Apes & Old World monkeys | 30 | Macaca nemestrina | pig-tailed macaque | 9545 | mMacNem1 | mMacNem1.hap1 | GCA_043159975.1 | GCF_043159975.1 | GCF_043159975.1 | Has X and Y | mMacNem1.hap2 | GCA_043161795.1 | CM091553.1 | Completed NCBI | SRX20928350;SRX20928351;SRX20928352;SRX20928353;SRX20928354;SRX20928355;SRX20928356;SRX20928357;SRX20928358;SRX20928359 | HiFi, Hifiasm Hi-C phasing | 621 | 22 | 3,116,288,670 | M | Endangered | Allen Institute | Trygve Bakken <trygveb@alleninstitute.org> | Erich Jarvis <ejarvis@rockefeller.edu> | Allen Institute | |||||||||||||
23 | m12 | Mammals | Supraprimates (Euarchontoglires) | Primates (Platyrrhines) | Cebidae | New World Monkeys | 30 | 132 | 4 | Callithrix jacchus | common marmoset | 9483 | 5 | mCalJac2 | mCalJac2.pri | GCA_049354715.1 | GCA_049354715.1 | Has X and Y | mCalJac1.pat, mCalJac1.mat | GCA_049354655.1, GCA_011100555.2, GCA_011078405.1 | in annotation queue | PRJNA516733 | SRX19907339;SRX19907342 | RSII, ONT, Verkko | 27 | 24 | 2,933,409,465 | M | Least Concern | VGP | Benedict Paten <bpaten@ucsc.edu> | Erich Jarvis <ejarvis@rockefeller.edu> | Strategic Priority Research Program of the Chinese Academy of Sciences, HHMI | PMID: 33910227 | ||||||||||
24 | m12 | Mammals | Supraprimates (Euarchontoglires) | Primates (Platyrrhines) | Cebidae | New World Monkeys | 30 | Saimiri boliviensis | Bolivian squirrel monkey | 27679 | mSaiBol1 | mSaiBol1.pri | GCA_048565385.1 | GCF_048565385.1 | GCF_048565385.1 | Has X and Y | mSaiBol1.alt | GCA_048565415.1 | CM109032.1 | Completed NCBI | HiFi, Hifiasm solo | 135 | 62 | 2,747,459,968 | M | Least Concern | Allen Institute | Trygve Bakken <trygveb@alleninstitute.org> | Erich Jarvis <ejarvis@rockefeller.edu> | Allen Institute | ||||||||||||||
25 | m12 | Mammals | Supraprimates (Euarchontoglires) | Primates (Platyrrhines) | Atelidae | New World Monkeys | 30 | Ateles marginatus | white-cheeked spider monkey | 1529884 | mAteMar1 | Hi-C issues, doing Hi-C over again | Endangered | Amazoomics : Genomics of Brazilian Biodiversity | Alexandre Aleixo <alexandre.aleixo@itv.org> | Sibelle Vilaca <sibelle.vilaca@itv.org> | Vale | |||||||||||||||||||||||||||
26 | m12 | Mammals | Supraprimates (Euarchontoglires) | Primates (Platyrrhines) | Pitheciidae | New World Monkeys | 30 | Chiropotes utahicki | Uta Hick's bearded saki | 280160 | mChiUta1 | mChiUta1.hap1 | Curated by Amazoomics, ready for submission | Endangered | Amazoomics : Genomics of Brazilian Biodiversity | Alexandre Aleixo <alexandre.aleixo@itv.org> | Sibelle Vilaca <sibelle.vilaca@itv.org> | Vale | ||||||||||||||||||||||||||
27 | m13 | Mammals | Supraprimates (Euarchontoglires) | Primates (Tarsiiformes) | Tarsiidae | Tarsiers | 66 | 14 | 1 | Carlito syrichta | Philippine tarsier | 1868482 | 3 | SRX392847 | Shearing Feb 15 2025. DNA processing Dec 2024. Paul Hime Nov 21 2024 University of Kansas, ready to ship in Dec 2. Kim AfricaBP fresh frozen Sep10 2024; William J. Murphy may have this species and other mammals. Will respond again in early 2023. San Diego Zoo; Field Museum suggested Museum of Natural History at the University of Kansas and the Cincinnati Museum's Collection and Research Center Duke Lemur Center sample not prepared well. Felix Grewe <fgrewe@fieldmuseum.org> Lawrence Heaney says contact Museum of Natural History at the University of Kansas and the Cincinnati Museum's Collection and Research Center. Contig only assembly GCA_027257055.1 | Threatened | VGP | Erich Jarvis <ejarvis@rockefeller.edu> | Paul Hime <paul.hime@wustl.edu> | HHMI | ||||||||||||||||||||||||
28 | m14 | Mammals | Supraprimates (Euarchontoglires) | Primates (Lorisoidea) | Lorisoidea | Loris, Galagos | 55 | 34 | 1 | Nycticebus coucang | sunda slow loris | 9470 | 4 | mNycCou1 | mNycCou1.pri | GCA_027406575.1 | GCF_027406575.1 | GCF_027406575.1 | Has X and Y | mNycCou1.alt | GCA_027406535.1 | None | Completed NCBI | ERX1403344;SRX104348;SRX104353;SRX104359;SRX104786 | HiFi, Hifiasm solo | 302 | 84 | 2,917,154,053 | M | Vulnerable | VGP | Erich Jarvis <ejarvis@rockefeller.edu> | Oliver Ryder <oryder@ucsd.edu> | HHMI | ||||||||||
29 | m15 | Mammals | Supraprimates (Euarchontoglires) | Primates (Lemuriformes) | Lemuroidea | Lemurs | 55 | 101 | 1 | Lemur catta | ring-tailed lemur | 9447 | 4 | mLemCat1 | mLemCat1.pri | GCA_020740605.1 | GCF_020740605.2 | GCF_020740605.2 | Has X and Y | mLemCat1.alt | GCA_020740595.1 | CM036502.1 | Completed NCBI | ERX1403305;SRX270664;SRX270665;SRX724899 | HiFi, Hifiasm solo | 395 | 185 | 2,245,601,549 | M | Endangered | VGP | Tomas Marques-Bonet <tomas.marques@upf.edu> | Marc Palmada Flores <marc.palmada@upf.edu> | "la Caixa" Foundation, European Union's Horizon 2020, HHMI | PMID: 35365833 | |||||||||
30 | m16 | Mammals | Supraprimates (Euarchontoglires) | Dermoptera | Cynocephalidae | Colugos | 80 | 2 | 1 | Cynocephalus volans | Philippine flying lemur | 110931 | 4 | mCynVol1 | mCynVol1.pri | GCA_027409185.1 | GCF_027409185.1 | GCF_027409185.1 | Has X and Y | mCynVol1.alt | GCA_027409165.1 | CM050047.1 | Completed NCBI | SRX21609207 | HiFi, Hifiasm solo | 246 | 130 | 2,814,418,120 | M | Least Concern | VGP | Felix Grew <fgrewe@fieldmuseum.org> | Erich Jarvis <ejarvis@rockefeller.edu> | HHMI | ||||||||||
31 | m17 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Erethizontidae) | Erethizontidae | Porcupines | 60 | 29 | 1 | Erethizon dorsatum | North American porcupine | 34844 | 4 | mEreDor1 | mEreDor1.pri | GCA_028451465.1 | GCA_028451465.1 | Has X and Y | mEreDor1.alt | GCA_028500835.1 | CM051845.1 | SRX2170058;SRX2170059 | CLR I, FALCON unzip | 393 | 116 | 2,432,147,792 | M | Least Concern | VGP | Felix Grew <fgrewe@fieldmuseum.org> | Bruce Patterson <bpatterson@fieldmuseum.org> | HHMI | ||||||||||||
32 | m18 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Ctenodactylidae) | Ctenodactylidae | Gundis, Squirrel-rat | 60 | 2 | 1 | Ctenodactylus gundi | common gundi | 10166 | 4 | mCteGun2 | mCteGun2.hap1 | GCA_048771875.1 | GCA_048771875.1 | Has X only | mCteGun2.hap2 | GCA_048771865.1 | ERX10650054;ERX10650055;ERX10650056;ERX10650057;ERX10650058;ERX10650059;ERX10650060;ERX10650061;ERX10650062;ERX10650063 | 652 | 535 | 2,184,404,205 | F | Least Concern | VGP | Erich Jarvis <ejarvis@rockefeller.edu> | Christopher Conroy <ondatra@berkeley.edu> | HHMI | ||||||||||||||
33 | m19 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Gliridae) | Gliridae | Dormice | 60 | 29 | 1 | Muscardinus avellanarius | common dormouse | 39082 | 4 | mMusAve1 | mMusAve1.pri | GCA_963383645.1 | GCA_963383645.1 | Has X and Y | mMusAve1.alt | GCA_963383665.1 | OY726581.1 | HiFi, Hifiasm solo | 2,018 | 213 | 2,497,520,702 | M | Least Concern | VGP | Astrid Böhne <a.boehne@leibniz-lib.de> | Mark Blaxter <mb35@sanger.ac.uk> | Wellcome Trust | PMID: 38911281 | ||||||||||||
34 | m20 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Sciuridae) | Sciuridae | Squirrels, Chipmunks | 55 | 285 | 7 | Sciurus vulgaris | Eurasian red squirrel | 55149 | 4 | mSciVul1.2 | mSciVul1.2.pri | GCA_902686455.2 | GCA_902686455.2 | Has X and Y | mSciVul1.2.alt | GCA_902685485.1 | LR822068.1 | SRX2170036;SRX2170037;SRX2170038 | CLR I, FALCON unzip | 1,808 | 639 | 2,878,607,543 | M | Least Concern | Sanger 25G | Mark Blaxter <mb35@sanger.ac.uk> | Richard Durbin <rd@sanger.ac.uk> | Wellcome Trust | PMID: 32587897 | |||||||||||
35 | m20 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Sciuridae) | Sciuridae | Squirrels, Chipmunks | 55 | Sciurus carolinensis | grey squirrel | 30640 | mSciCar1 | mSciCar1.2.pri | GCA_902686445.2 | GCF_902686445.1 | GCA_902686445.2 | Has X and Y | mSciCar1.2.alt | GCA_902685475.1 | Completed NCBI | CLR I, FALCON unzip | 2,576 | 752 | 2,815,397,268 | M | Least Concern | Sanger 25G | Mark Blaxter <mb35@sanger.ac.uk> | Richard Durbin <rd@sanger.ac.uk> | Wellcome Trust | PMID: 33215047 | ||||||||||||||
36 | m20 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Sciuridae) | Sciuridae | Squirrels, Chipmunks | 55 | Urocitellus parryii | Arctic ground squirrel | 9999 | mUroPar1 | mUroPar1.hap1 | GCA_045843805.1 | GCA_045843805.1 | Has X and Y | mUroPar1.hap2 | GCA_045843765.1 | CM099878.1 | HiFi, Hifiasm Hi-C phasing | 3,223 | 18 | 2,935,776,410 | M | Least Concern | Allen Institute | Trygve Bakken <trygveb@alleninstitute.org> | Erich Jarvis <ejarvis@rockefeller.edu> | Allen Institute, HHMI | ||||||||||||||||
37 | m20 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Sciuridae) | Sciuridae | Squirrels, Chipmunks | 55 | Spermophilus citellus | European ground squirrel | 9997 | mSpeCit3 | mSpeCit3.pri | GCA_964194105.1 | GCA_964194105.1 | Has X only | mSpeCit3.alt | GCA_964194095.1 | OZ077398.1 | HiFi, Hifiasm solo | 1,934 | 498 | 3,090,049,053 | F | Endangered | ERGA | Alexandros Triantafyllidis <atriant@bio.auth.gr> | Mark Blaxter <mb35@sanger.ac.uk> | Wellcome Trust | ||||||||||||||||
38 | m20 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Sciuridae) | Sciuridae | Squirrels, Chipmunks | 55 | Callospermophilus lateralis | golden-mantled ground squirrel | 76772 | mCalLat2 | mCalLat2.hap1 | GCA_048772815.1 | GCA_048772815.1 | Has X and Y | mCalLat2.hap2 | GCA_048772825.1 | in annotation queue | HiFi, Hifiasm Hi-C phasing | 9,535 | 8,087 | 4,646,974,320 | M | Least Concern | Cohen Lab | Paul Cohen <pcohen@rockefeller.edu> | Erich Jarvis <ejarvis@rockefeller.edu> | Rockefeller University | ||||||||||||||||
39 | m20 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Sciuridae) | Sciuridae | Squirrels, Chipmunks | 55 | Marmota flaviventris | yellow bellied marmot | 93162 | mMarFla1 | mMarFla1.hap1 | GCA_047511675.1 | GCF_047511675.1 | GCF_047511675.1 | Has X and Y | mMarFla1.hap2 | GCA_047512175.1 | CM105229.1 | Completed NCBI | HiFi, Hifiasm Hi-C phasing | 1,143 | 813 | 2,704,651,887 | M | Least Concern | Cohen Lab | Paul Cohen <pcohen@rockefeller.edu> | Erich Jarvis <ejarvis@rockefeller.edu> | Rockefeller University | ||||||||||||||
40 | m20 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Sciuridae) | Sciuridae | Squirrels, Chipmunks | 55 | Ictidomys tridecemlineatus | thirteen-lined ground squirrel | 43179 | mIctTri1 | mIctTri1.hap1 | GCA_052094955.1 | Has X and Y | mIctTri1.hap2 | GCA_052094965.1 | CM125502.1 | Ready (9/10/2025) | HiFi, Hifiasm Hi-C phasing | 6,723 | 5,279 | 3,144,977,123 | M | Least Concern | Cohen Lab | Paul Cohen <pcohen@rockefeller.edu> | Erich Jarvis <ejarvis@rockefeller.edu> | Rockefeller University | ||||||||||||||||
41 | m21 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Aplodontiidae) | Aplodontiidae | Mountain Beaver | 55 | 1 | 1 | Aplodontia rufa | mountain beaver | 51342 | 3 | Ryan found out he does not have cell line, and still hard to get a fresh sample. Ryan Langlois has cell line in Minnesota. Kathleen to contact 12/2023. Antoinette Piaggio and Klaus, sample too low DNA size - get again, but did not respond; Erich email; Bob Murphy supplied Aplodontiidae for Zoonomia | Least Concern | |||||||||||||||||||||||||||||
42 | m22 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Muridae) | Muridae | Mice, Rats | 50 | 1300 | 7 | Acomys russatus | golden spiny mouse | 60746 | 4 | mAcoRus1 | mAcoRus1.pri | GCA_903995435.1 | GCF_903995435.1 | GCF_903995435.1 | Has X only | Not provided | Completed NCBI | ERX9827169;ERX9827170;ERX9827171;ERX9827172;ERX9827173;ERX9827174;SRX13395815;SRX13395816;SRX13395817;SRX13395818 | CLR, FALCON unzip | 1,502 | 623 | 2,301,522,284 | F | Least Concern | VGP | Thomas Keane <tk2@ebi.ac.uk> | Richard Durbin <rd@sanger.ac.uk> | Wellcome Trust | ||||||||||||
43 | m22 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Muridae) | Muridae | Mice, Rats | 50 | Apodemus sylvaticus | European woodmouse | 10129 | mApoSyl1 | mApoSyl1.pri | GCA_947179515.1 | GCF_947179515.1 | GCF_947179515.1 | Has X and Y | mApoSyl1.alt | GCA_947179525.1 | Completed NCBI | ERX9439056;ERX9439057;ERX9439058;ERX9439059;ERX9439060;ERX9439061;ERX9439062;ERX9439063;ERX9439064;ERX9439065 | HiFi, Hifiasm solo | 1,627 | 498 | 2,889,801,511 | M | Least Concern | DToL | Sarah C L Knowles <sarah.knowles@zoo.ox.ac.uk> | Mark Blaxter <mb35@sanger.ac.uk> | Wellcome Trust | PMID: 39099644 | |||||||||||||
44 | m22 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Muridae) | Muridae | Mice, Rats | 50 | Arvicanthis niloticus | Nile rat | 61156 | mArvNil1 | mArvNil1.pat | GCA_011762505.3 | GCA_011762505.3 | Has X and Y | mArvNil1.mat | GCA_011750645.1 | PRJNA516733 | SRX18639742;SRX18639743;SRX18639744;SRX18639745;SRX18639746;SRX18639747;SRX18639748;SRX18639749;SRX18639750;SRX18639751 | CLR, TrioCanu | 3,219 | 1,595 | 2,496,761,438 | M | Least Concern | VGP | Yury Bukhman <YBukhman@morgridge.org> | Erich Jarvis <ejarvis@rockefeller.edu> | William K. Bowes Jr. Foundation, HHMI | PMID: 36344967 | ||||||||||||||
45 | m22 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Muridae) | Muridae | Mice, Rats | 50 | Rattus norvegicus | Norway rat | 10116 | mRatNor1 | mRatNor1.pri | GCA_015227675.2 | GCF_015227675.2 | GCF_015227675.2 | Has X and Y | mRatNor1.alt | GCA_015244455.1 | AY172581.1 | Completed NCBI | SRX9572806;SRX9572807;SRX9572808;SRX9572809;SRX9572810;SRX9572811;SRX9572812;SRX9572813;SRX9572814;SRX9572815 | CLR, FALCON unzip | 757 | 176 | 2,647,915,728 | M | Least Concern | DToL | Kerstin Howe <kj2@sanger.ac.uk> | Mark Blaxter <mb35@sanger.ac.uk> | Wellcome Trust | PMID: 34660910 | ||||||||||||
46 | m22 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Muridae) | Muridae | Mice, Rats | 50 | Micromys minutus | European harvest mouse | 13151 | mMicMin1 | mMicMin1.pri | GCA_963924665.1 | GCA_963924665.1 | Has X only | mMicMin1.alt | GCA_963924645.1 | OZ004814.1 | HiFi, Hifiasm solo | 2,914 | 894 | 2,651,787,409 | F | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Michelle F O'Brien <michelle.obrien@wwt.org.uk> | Wellcome Trust | PMID: 39411465 | |||||||||||||||
47 | m22 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Muridae) | Muridae | Mice, Rats | 50 | Mus musculus | house mouse | 10090 | mMusMuc1.1 | mMusMuc1.pri | GCA_949316315.1 | GCA_949316315.1 | Has X only | mMusMuc1.alt | GCA_949316305.1 | OX439034.1 | HiFi, Hifiasm solo | 280 | 179 | 2,770,968,735 | F | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Wellcome Trust | |||||||||||||||||
48 | m22 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Muridae) | Muridae | Mice, Rats | 50 | Acomys minous | Crete spiny mouse | 83528 | mAcoMin1 | mAcoMin1.pri | GCA_964271855.1 | GCA_964271855.1 | Needs sex chr named | HiFi, Hifiasm solo | 297 | 113 | 2,350,237,540 | F | No alternate, being updated by ERGA lab GCA_964271855.3; need more metadata on assembly protocol | ERGA | William,W. | BGE | ||||||||||||||||||||
49 | m59 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Cricetidae) | Cricetidae | Hamsters, New World rats & mice, muskrats, voles | 50 | 681 | 7 | Microtus pennsylvanicus | Eastern meadow vole | 10058 | 4 | mMicPen1 | mMicPen1.hap1 | GCA_037038515.1 | GCF_037038515.1 | GCF_037038515.1 | Has X and Y | mMicPen1.hap2 | GCA_037039175.1 | Completed NCBI | PRJNA1273673 | SRX9686736;SRX9686737;SRX9686738;SRX9686745;SRX9686752;SRX9686758;SRX9686759;SRX9686760;SRX9686761;SRX9686762 | HiFi, Hifiasm Hi-C phasing | 241 | 181 | 2,369,135,991 | M | Least Concern | VGP | Lauren O'Connell <loconnel@stanford.edu> | Erich Jarvis <ejarvis@rockefeller.edu> | Stanford | ||||||||||
50 | m59 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Cricetidae) | Cricetidae | Hamsters, New World rats & mice, muskrats, voles | 50 | Onychomys torridus | Southern grasshopper mouse | 38674 | mOncTor1 | mOncTor1.pri | GCA_903995425.1 | GCF_903995425.1 | GCF_903995425.1 | Has X only | Completed NCBI | ERX10911024;ERX10911025;ERX10911026;ERX10911029;ERX10911034;ERX1785503;ERX1785504;ERX1785505;ERX1785506;ERX1785507 | CLR I, FALCON | 5,088 | 2,949 | 2,468,394,440 | F | Least Concern | VGP | Thomas Keane <tk2@ebi.ac.uk> | Richard Durbin <rd@sanger.ac.uk> | Wellcome Trust | ||||||||||||||||
51 | m59 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Cricetidae) | Cricetidae | Hamsters, New World rats & mice, muskrats, voles | 50 | Arvicola amphibius | European water vole | 1047088 | mArvAmp1 | mArvAmp1.pri | GCA_903992535.2 | GCF_903992535.2 | GCF_903992535.2 | Has X only | mArvAmp1.alt | GCA_903992525.1 | Completed NCBI | SRX5914028;SRX5914029;SRX5914030;SRX5914031;SRX5914032;SRX5914033 | CLR, FALCON unzip | 1,085 | 215 | 2,297,766,297 | F | Least Concern | Sanger 25G | Daniel Mead <da2@sanger.ac.uk> | Richard Durbin <rd@sanger.ac.uk> | Wellcome Trust | PMID: 35600244 | |||||||||||||
52 | m59 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Cricetidae) | Cricetidae | Hamsters, New World rats & mice, muskrats, voles | 50 | Chionomys nivalis | European snow vole | 269649 | mChiNiv1 | mChiNiv1.pri | GCA_950005125.1 | GCF_950005125.1 | GCF_950005125.1 | Has X and Y | mChiNiv1.alt | GCA_950005115.1 | Completed NCBI | ERX10349547;SRX17979308;SRX17979309 | HiFi hifiasm, solo | 358 | 161 | 2,393,406,913 | M | Least Concern | ERGA | Mark Blaxter <mb35@sanger.ac.uk> | Franc Janžekovič <franc.janzekovic@um.si> | Wellcome Trust | submitted | |||||||||||||
53 | m59 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Cricetidae) | Cricetidae | Hamsters, New World rats & mice, muskrats, voles | 50 | Peromyscus maniculatus | deer mouse | 10042 | mPerMan1 | mPerMan1.pri | GCA_026229955.1 | GCA_026229955.1 | Needs curation GCA_026229955.1 | mPerMan1.alt | SRX22077833;SRX22077834;SRX22077835;SRX22077836;SRX22077837;SRX22077838;SRX22077839;SRX22077840;SRX22077841;SRX22077842 | HiFi hifiasm, solo | 2,082 | 1,838 | 2,847,741,276 | M | In curation at RU Aug 2025. GCA_026229955.1 Needs curation from CCGP | Least Concern | CCGP | Bradley Shaffer <brad.shaffer@ucla.edu> | Chris J Conroy<ondatra@berkeley.edu> | State of California | ||||||||||||||||
54 | m59 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Cricetidae) | Cricetidae | Hamsters, New World rats & mice, muskrats, voles | 50 | Peromyscus gossypinus | cotton mouse | 42411 | mPerGos1 | In curation queue at RU | Least Concern | Revive & Restore | Ben Novak <ben@reviverestore.org> | Erich Jarvis <ejarvis@rockefeller.edu> | Revive & Restore | |||||||||||||||||||||||||||
55 | m59 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Cricetidae) | Cricetidae | Hamsters, New World rats & mice, muskrats, voles | 50 | Neotoma floridana | Eastern woodrat | 42409 | mNeoFlo1 | mNeoFlo1.hap1 | GCA_050000055.1 | GCA_050000055.1 | Has X and Y | mNeoFlo1.hap2 | GCA_050000045.1 | CM113812.1 | HiFi, Hifiasm Hi-C phasing | 1,535 | 1,381 | 3,228,206,949 | M | Least Concern | Revive & Restore | USFW | Ben Novak <ben@reviverestore.org> | Erich Jarvis <ejarvis@rockefeller.edu> | Revive & Restore | |||||||||||||||
56 | m23 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Dipodidae) | Dipodidae | Jumping mice | 50 | 50 | 1 | Jaculus jaculus | Lesser Egyptian jerboa | 51337 | 4 | mJacJac1 | mJacJac1.mat | GCA_020740685.1 | GCF_020740685.1 | GCF_020740685.1 | Has X and Y | mJacJac1.pat | GCA_020740715.1 | Completed NCBI | SRX19392342;SRX19392343;SRX19392344;SRX19392345;SRX19392346;SRX19392347;SRX19392348;SRX19392349;SRX19392350;SRX19392351 | CLR II, TrioCanu | 716 | 160 | 2,863,865,261 | M | Least Concern | VGP | Kim Cooper <kcooper@ucsd.edu> | Erich Jarvis <ejarvis@rockefeller.edu> | NIH, NIAMS | |||||||||||
57 | m24 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Anomaluridae) | Anomaluridae | Flying squirrels | 55 | 7 | 1 | Anomalurus beecrofti | Beecroft's flying squirrel | 1082180 | 3 | Adam Ferguson at Field Museum has frozen sample Nov 27 2024. Jeff has sample and maybe reference genome Nov 25 2024; contacted Larry Heany. Nov 24 2024 Bowman, Jeff (MNRF) <Jeff.Bowman@ontario.ca> Sep 14 2024; Ryan Sep 2024; Cynthia Steiner does not have sample and did not ship to RU Aug 16 2024. Ryan A. Langlois has contact at Wisconson Jul 4 2024. Sasha Nawar putting Erich in contact with Jeff Bowman Jul 2024. will sequence limited sample from Cyntia Steiner at San Diego Zoo, at Rockefeller Feb 2024. AfricaBP; no sample of Feb 14, 2023; LSU, Mark Swanson; 2019-01-08 SAMN10715114 (he said stored in EToH only at room temp) | Least Concern | |||||||||||||||||||||||||||||
58 | m25 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Pedetidae) | Pedetidae | Springhares | 55 | 2 | 1 | Pedetes capensis | South African springhare | 10023 | 3 | New sample did not work for Hi-C. Aug 2025. Kim Labuschagne AfricaBP gave recently to Inqaba Nov 2024; RU blood sample from Cynthia Steiner did not work and she does not have another sample; asked for replacement sample Aug 16 2024. Try another sample. Hold on AfricaBP Ntanga has cells; Hi-C only; older sample from Cynthia thawed in shipment. | Least Concern | AfricaBP | VGP | |||||||||||||||||||||||||||
59 | m26 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Geomyoidea) | Geomyoidea | Gophers, Kangaroo rats | 59 | 94 | 1 | Thomomys bottae | Botta's pocket gopher | 10013 | 4 | mThoBot2 | mThoBot2.hap1 | GCA_031878675.1 | GCA_031878675.1 | Has X and Y | mThoBot2.hap2, mThoBot1.0.p | GCA_031878665.1, GCA_024803745.1 | mThoBot1.0.a | GCA_024803775.1 | CM063115.1 | HiFi, Hifiasm Hi-C phasing | 1,405 | 630 | 2,025,650,949 | M | Chris J Conroy<ondatra@berkeley.edu>; can you add the MVZ catalog number to the Biosample record? For this gopher, it is MVZ:Mamm:179317 | Least Concern | CCGP | Bradley Shaffer <brad.shaffer@ucla.edu> | Chris J Conroy<ondatra@berkeley.edu> | State of California | ||||||||||
60 | m27 | Mammals | Supraprimates (Euarchontoglires) | Rodentia (Castoridae) | Castoridae | Beavers | 59 | 2 | 1 | Castor canadensis | North American beaver | 51338 | 4 | mCasCan1 | mCasCan1.hap1 | GCA_047511655.1 | GCF_047511655.1 | GCF_047511655.1 | Has X only | mCasCan1.hap2 | GCA_047511605.1 | CM105230.1 | Completed NCBI | PRJNA1264479 | SRX13395829;SRX13395830;SRX13395831;SRX13395832;SRX13396073;SRX13396074;SRX13396075;SRX13396076;SRX13396077;SRX13396078 | HiFi, Hifiasm Hi-C phasing | 682 | 501 | 2,828,072,390 | F | Least Concern | VGP | Erich Jarvis <ejarvis@rockefeller.edu> | Ryan Langlois <langlois@umn.edu> | HHMI | |||||||||
61 | m28 | Mammals | Supraprimates (Euarchontoglires) | Lagomorpha (Leporidae) | Leporidae | Rabbits, Hares | 49 | 60 | 1 | Oryctolagus cuniculus | European rabbit | 9986 | 4 | mOryCun1 | mOryCun1.pri | GCA_964237555.1 | GCF_964237555.1 | GCF_964237555.1 | Has X only | mOryCun1.alt | GCA_964237575.1 | Completed NCBI | SRX18647333;SRX18647334;SRX18647335;SRX18647336;SRX18647337;SRX18647338;SRX18647339;SRX18647340;SRX22051787;SRX22051788 | Hifi, Hifiasm solo | 2,497 | 221 | 2,804,657,419 | F | Endangered | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Michelle F O'Brien <michelle.obrien@wwt.org.uk> | Wellcome Trust | |||||||||||
62 | m29 | Mammals | Supraprimates (Euarchontoglires) | Lagomorpha (Ochotonidae) | Ochotonidae | Pikas | 49 | 30 | 1 | Ochotona princeps | American pika | 9978 | 4 | mOchPri1 | mOchPri1.hap1 | GCA_030435755.1 | GCF_030435755.1 | GCF_030435755.1 | Has X and Y | mOchPri1.hap2 | GCA_030435715.1 | Completed NCBI | HiFi, Hifiasm Hi-C phasing | 6,296 | 5,864 | 2,555,444,530 | M | Least Concern | VGP | Erich Jarvis <ejarvis@rockefeller.edu> | John Demboski <john.demboski@ucdenver.edu> | HHMI | ||||||||||||
63 | m30 | Mammals | Supraprimates (Euarchontoglires) | Scandentia (Tupaiidae) | Tupaiidae | Treeshrews | 63 | 19 | 1 | Tupaia tana | large treeshrew | 70687 | 4 | mTupTan1 | mTupTan1.pri | GCA_026018925.1 | GCA_026018925.1 | Needs curation GCA_026018925.1 high priority | CLR I, FALCON unzip | 2,385 | 1,197 | 2,948,277,345 | UN | In curation at RU Aug 2025; conducted by UC Davis Harris Lewin | Least Concern | VGP | Harris Lewin <lewin@ucdavis.edu> | Joana Damas<joanadamas@gmail.com> | PacBio, Dovetail, Robert and UC Davis Rosabel Osborne Endowment. | |||||||||||||||
64 | m31 | Mammals | Supraprimates (Euarchontoglires) | Scandentia (Ptilocercidae) | Ptilocercidae | Pen-tailed treeshrew | 63 | 1 | 1 | Ptilocercus lowii | pen-tailed treeshrew | 320338 | 2 | Faisal Ali Bin Anwarali Khan has a sample Nov 2024. Cynthia Wang-Claypool, is reaching out to her contacts in Indonesia and Thailand Feb 7 2025. Has as sample from 2008, contacte again Nov 24, 2024. Faisal Kahn Sep 15 2024. William J. Murphy looking into. Mark Swanson said his sample stored only in EToH at room temp (not likely good) | Least Concern | |||||||||||||||||||||||||||||
65 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Phocoenidae | Whales, dolphines, orcas | 54 | 90 | 27 | Phocoena sinus | vaquita | 42100 | 4 | mPhoSin1 | mPhoSin1.pri | GCA_008692025.1 | GCF_008692025.1 | GCF_008692025.1 | Has X only | mPhoSin1.alt | GCA_008692045.1 | Completed NCBI | PRJNA516733 | SRX7696400;SRX7696401 | CLR I, FALCON unzip | 272 | 64 | 2,371,524,154 | F | Critically Endangered | VGP | Cetacean GP | Phil Morin <phillip.morin@noaa.gov> | Erich Jarvis <ejarvis@rockefeller.edu> | NOAA | PMID: 33089966 | ||||||||
66 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Phocoenidae | Whales, dolphines, orcas | 54 | Phocoena phocoena | harbor porpoise | 9742 | mPhoPho1 | mPhoPho1.pri | GCA_963924675.1 | GCF_963924675.1 | GCF_963924675.1 | Has X only | mPhoPho1.alt | GCA_963924725.1 | OZ004779.1 | Completed NCBI | HiFi, Hifiasm solo | 1,406 | 440 | 2,512,729,496 | F | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Nick Davison <Nick.Davison@glasgow.ac.uk> | Wellcome Trust | ||||||||||||||
67 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Delphinidae | Whales, dolphines, orcas | 54 | Tursiops truncatus | bottlenose dolphin | 9739 | mTurTru1 | mTurTru1.mat | GCA_011762595.2 | GCF_011762595.2 | GCF_011762595.2 | Has X and Y | mTurTru1.pat | GCA_011762515.1 | EU557093.1 | Completed NCBI | SRX8998729;SRX8998730;SRX8998731;SRX8998732;SRX8998733;SRX8998734;SRX8998735;SRX8998736;SRX8998737;SRX8998738 | CLR I, TrioCanu | 1,036 | 362 | 2,378,522,213 | M | Least Concern | VGP | Cetacean GP | John Demboski <john.demboski@ucdenver.edu> | Brigid Maloney <bmaloney@rockefeller.edu> | HHMI, Rockefeller University | ||||||||||||
68 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Delphinidae | Whales, dolphines, orcas | 54 | Pseudorca crassidens | false killer whale | 82174 | mPseCra1 | mPseCra1.hap1 | GCA_039906515.1 | GCF_039906515.1 | GCF_039906515.1 | Has X and Y | mPseCra1.hap2 | GCA_039906525.1 | CM078552.1 | Completed NCBI | HiFi, Hifiasm Hi-C phasing | 562 | 439 | 2,674,608,476 | M | Near Threatened | Cetacean GP | VGP | Phil Morin <phillip.morin@noaa.gov> | Erich Jarvis <ejarvis@rockefeller.edu> | Revive & Restore | |||||||||||||
69 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Delphinidae | Whales, dolphines, orcas | 54 | Peponocephala electra | melon-headed whale | 103596 | mPepEle1 | mPepEle1.hap1 | GCA_051427945.1 | GCA_051427945.1 | Has X and Y | mPepEle1.hap2 | GCA_051427955.1 | SRX14357998 | HiFi, Hifiasm Hi-C phasing | 288 | 204 | 2,540,361,747 | M | Least Concern | Individual | Zhenpeng Yu <yuzhenpeng2013@163.com> | Shixia Xu <<xushixia@njnu.edu.cn> | National Natural Science Foundation of China | PMID: 36146916 | |||||||||||||||
70 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Delphinidae | Whales, dolphines, orcas | 54 | Lagenorhynchus acutus | Atlantic white-sided dolphin | 90246 | mLagAcu1 | mLagAcu1.hap1 | GCA_964270905.1 | GCA_964270905.1 | Has X and Y | mLagAcu1.hap2 | GCA_964270935.1 | OZ185479.1 | HiFi, Hifiasm Hi-C phasing | 1,932 | 898 | 2,676,193,030 | M | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Nick Davison <Nick.Davison@glasgow.ac.uk> | Wellcome Trust | ||||||||||||||||
71 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Delphinidae | Whales, dolphines, orcas | 54 | Orcinus orca | killer whale | 9733 | mOrcOrc1 | mOrcOrc1.pri | GCA_937001465.1 | GCF_937001465.1 | GCF_937001465.1 | Has X only | mOrcOrc1.alt | GCA_937001455.1 | NC_064558.1 | Completed NCBI | SRX5120176 | HiFi, Hifiasm solo | 571 | 448 | 2,647,351,467 | F | Not evaluated | DToL | Cetacean GP | Mark Blaxter <mb35@sanger.ac.uk> | Andy Foote <andrew.foote@ntnu.no> | Wellcome Trust | PMID: 36974126 | |||||||||||
72 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Delphinidae | Whales, dolphines, orcas | 54 | Lagenorhynchus albirostris | white-beaked dolphin | 27610 | mLagAlb1 | mLagAlb1.pri | GCA_949774975.1 | GCF_949774975.1 | GCF_949774975.1 | Has X only | mLagAlb1.alt | GCA_949774935.1 | NC_083094.1 | Completed NCBI | ERX11235631;ERX1403317;ERX1403340 | HiFi, Hifiasm solo | 1,480 | 410 | 2,544,835,795 | F | Least Concern | DToL | Cetacean GP | Mark Blaxter <mb35@sanger.ac.uk> | Phil Morin <phillip.morin@noaa.gov> | Wellcome Trust | PMID: 39635243 | |||||||||||
73 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Delphinidae | Whales, dolphines, orcas | 54 | Globicephala melas | long-finned pilot whale | 9731 | mGloMel1 | mGloMel1.pri | GCA_963455315.2 | GCF_963455315.2 | GCF_963455315.2 | Has X and Y | mGloMel1.alt | GCA_963455345.2 | OY734062.1 | Completed NCBI | ERX11235682;SRX13278360;SRX13278361;SRX13278362;SRX13278363;SRX5120178;SRX5120179 | HiFi, Hifiasm solo | 2,077 | 993 | 2,651,292,441 | M | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Nick Davison <Nick.Davison@glasgow.ac.uk> | Wellcome Trust | |||||||||||||
74 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Delphinidae | Whales, dolphines, orcas | 54 | Grampus griseus | Risso's dolphin | 83653 | mGraGri1 | mGraGri1.hap1 | GCA_964374135.1 | GCA_964374135.1 | Has X and Y | mGraGri1.hap2 | GCA_964374185.1 | OZ206336.1 | HiFi, Hifiasm Hi-C phasing | 2,283 | 1,145 | 2,667,065,542 | M | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Nick Davison <Nick.Davison@glasgow.ac.uk> | Wellcome Trust | ||||||||||||||||
75 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Iniidae | Whales, dolphines, orcas | 54 | Inia geoffrensis | Amazon river dolphin | 9725 | mIniGeo1 | mIniGeo1.hap1 | GCA_036417435.1 | GCA_036417435.1 | Has X and Y | mIniGeo1.hap2 | GCA_036417475.1 | CM070922.1 | CLR I, FALCON unzip | 1,187 | 903 | 2,749,362,370 | M | Endangered | Cetacean GP | VGP | Michael Hiller <michael.hiller@senckenberg.de> | Phil Morin <phillip.morin@noaa.gov> | Revive & Restore, LOEWE Centre for Translational Biodiversity Genomics, HHMI | |||||||||||||||
76 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Iniidae | Whales, dolphines, orcas | 54 | Delphinus delphis | saddleback dolphin | 9728 | mDelDel1.1 | mDelDel1.pri | GCA_949987515.2 | GCF_949987515.2 | GCF_949987515.2 | Has X and Y | mDelDel1.alt | GCA_949987525.2 | Completed NCBI | ERX11235633;ERX1403334;ERX1403339;ERX1403341;SRX18343405;SRX18360486;SRX18370762;SRX18371481;SRX18371618 | Hifi, Hifiasm solo | 1,599 | 631 | 2,663,533,373 | M | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Nick Davison <Nick.Davison@glasgow.ac.uk> | Wellcome Trust | ||||||||||||||
77 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenopteridae | Whales, dolphines, orcas | 54 | Balaenoptera musculus | blue whale | 9771 | mBalMus1 | mBalMus1.3.pri | GCA_009873245.3 | GCF_009873245.2 | GCA_009873245.3 | Has X and Y | mBalMus1.3.alt | GCA_008658375.2 | X72204.1 | Completed NCBI | PRJNA516733 | SRX10710728;SRX5087289;SRX6360705;SRX7696402 | CLR I, FALCON unzip | 973 | 106 | 2,374,868,943 | M | Endangered | VGP | Yury Bukhman <YBukhman@morgridge.org> | Ron Stewart <RStewart@morgridge.org> | Morgridge Institute for Research. NHGRI | PMID: 38376487 | |||||||||||
78 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenopteridae | Whales, dolphines, orcas | 54 | Stenella coeruleoalba | striped dolphin | 9737 | mSteCoe1.1 | mSteCoe1.pri | GCA_951394435.1 | GCA_951394435.1 | Has X and Y | mSteCoe1.alt | GCA_951394445.1 | OX596408.1 | ERX11235632 | HiFi, Hifiasm solo | 1,631 | 638 | 2,691,423,227 | M | Least Concern | DToL | Cetacean GP | Mark Blaxter <mb35@sanger.ac.uk> | Phil Morin <phillip.morin@noaa.gov> | Wellcome Trust | PMID: 39811706 | |||||||||||||
79 | m33 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenopteridae | Whales, dolphines, orcas | 54 | Eschrichtius robustus | gray whale | 9764 | mEscRob2 | mEscRob2.pri | GCA_028021215.1 | GCF_028021215.1 | GCF_028021215.1 | Has X and Y | mEscRob2.alt | GCA_028021475.1 | CM051712.1 | Completed NCBI | SRX10234837;SRX10234838 | HiFi, Hifiasm solo | 983 | 702 | 2,982,434,994 | M | Least Concern | Cetacean GP | Phil Morin <phillip.morin@noaa.gov> | Erich Jarvis <ejarvis@rockefeller.edu> | NOAA | |||||||||||||
80 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenopteridae | Whales, dolphines, orcas | 54 | Balaenoptera ricei | Rice's whale | 2746895 | mBalRic1 | mBalRic1.hap2 | GCA_028023285.1 | GCF_028023285.1 | GCF_028023285.1 | Has X only | mBalRic1.hap1 | GCA_028017805.1 | MT asm failed | Completed NCBI | SRX21609210;SRX21609211 | HiFi, Hifiasm Hi-C phasing | 1,108 | 774 | 2,678,442,663 | F | Critically Endangered | Cetacean GP | Phil Morin <phillip.morin@noaa.gov> | Erich Jarvis <ejarvis@rockefeller.edu> | NOAA | |||||||||||||
81 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenopteridae | Whales, dolphines, orcas | 54 | Balaenoptera acutorostrata | common minke whale | 9767 | mBalAcu1.1 | mBalAcu1.pri | GCA_949987535.1 | GCF_949987535.1 | GCF_949987535.1 | Has X only | mBalAcu1.alt | GCA_950005055.1 | Not present | Completed NCBI | DRX363218;DRX363219;DRX363220;DRX363221;DRX363222;DRX363223;DRX363224;DRX363225;DRX363226;ERX11235629 | HiFi, Hifiasm solo | 2,552 | 1,375 | 2,772,901,778 | F | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Phil Morin <phillip.morin@noaa.gov> | Wellcome Trust | PMID: 39925658 | ||||||||||||
82 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenopteridae | Whales, dolphines, orcas | 54 | Megaptera novaeangliae | humpback whale | 9773 | mMegNov1 | mMegNov1.pri | GCA_041834305.1 | GCA_041834305.1 | Has X and Y | HiFi, Hifiasm solo | 1,443 | 1,355 | 3,146,604,256 | M | Need to do QC and curation of the other haplotype | Least Concern | Individual | Maria-Vittoria Carminati <Maria-Vittoria.Carminati@colorado.edu> | Nolan Kane <Nolan.Kane@Colorado.EDU> | experiment.com | PMID: 39389970 | |||||||||||||||||
83 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenopteridae | Whales, dolphines, orcas | 54 | Balaenoptera physalus | finback whale | 9770 | mBalPhy1 | mBalPhy1.hap1 | GCA_965194825.1 | GCA_965194825.1 | Has X and Y | mBalPhy1.hap2 | GCA_965194765.1 | OZ239533.1 | HiFi, Hifiasm Hi-C phasing | 4,127 | 2,611 | 3,442,538,501 | M | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Nick Davison <Nick.Davison@glasgow.ac.uk> | Wellcome Trust | ||||||||||||||||
84 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenopteridae | Whales, dolphines, orcas | 54 | Balaenoptera borealis | sei whale | 9768 | mBalBor1 | mBalBor1.hap1 | GCA_965194805.1 | GCA_965194805.1 | Has X only | mBalBor1.hap2 | GCA_965194725.1 | OZ239556.1 | HiFi, Hifiasm Hi-C phasing | 3,750 | 2,571 | 3,234,557,085 | F | Vulnerable | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Nick Davison <Nick.Davison@glasgow.ac.uk> | Wellcome Trust | ||||||||||||||||
85 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Ziphiidae | Whales, dolphines, orcas | 54 | Mesoplodon densirostris | Blainville's beaked whale | 48708 | mMesDen1 | mMesDen1.pri | GCA_025265405.1 | GCF_025265405.1 | GCF_025265405.1 | Has X and Y | mMesDen1.alt | GCA_025094165.1 | KF032860.2 | Completed NCBI | SRX21609212 | HiFi, Hifiasm solo | 170 | 73 | 2,683,375,131 | M | Least Concern | Cetacean GP | Phil Morin <phillip.morin@noaa.gov> | Erich Jarvis <ejarvis@rockefeller.edu> | NOAA | |||||||||||||
86 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Ziphiidae | Whales, dolphines, orcas | 54 | Mesoplodon bidens | Sowerby's beaked whale | 48745 | mMesBid2 | mMesBid2.hap1 | GCA_964165515.1 | GCA_964165515.1 | Has X and Y | mMesBid2.hap2 | GCA_964148845.1 | OZ073234.1 | HiFi, Hifiasm Hi-C phasing | 2,697 | 1,602 | 2,999,098,505 | M | Least Concern | ERGA | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Anna Roos <anro@natur.gl> | Wellcome Trust | |||||||||||||||
87 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Ziphiidae | Whales, dolphines, orcas | 54 | Mesoplodon mirus | True's beaked whale | 52113 | mMesMir1 | mMesMir1.hap1 | GCA_964341445.1 | GCA_964341445.1 | Has X only | mMesMir1.hap2 | GCA_964341485.1 | OZ205435.1 | HiFi, Hifiasm Hi-C phasing | 3,996 | 2,756 | 3,442,403,058 | F | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Nick Davison <Nick.Davison@glasgow.ac.uk> | Wellcome Trust | ||||||||||||||||
88 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Ziphiidae | Whales, dolphines, orcas | 54 | Hyperoodon ampullatus | North Atlantic bottlenose whale | 48744 | mHypAmp2.1 | mHypAmp2.pri | GCA_949752795.1 | GCA_949752795.1 | Has X only | mHypAmp2.pri | GCA_949752845.1 | OX457076.1 | ERX11235623 | HiFi, Hifiasm solo | 1,855 | 757 | 2,828,760,712 | F | Near Threatened | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Laura Joan Feyrer <ljfeyrer@dal.ca> | Wellcome Trust | PMID: 39649623 | ||||||||||||||
89 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Kogiidae | Whales, dolphines, orcas | 54 | Kogia breviceps | pygmy sperm whale | 27615 | mKogBre1 | mKogBre1.hap1 | GCA_026419965.1 | GCF_026419965.1 | GCF_026419965.1 | Has X only | mKogBre1.hap2 | GCA_026419985.1 | AJ554055.1 | Completed NCBI | HiFi, Hifiasm Hi-C phasing | 723 | 580 | 2,555,838,840 | F | Least Concern | Cetacean GP | Phil Morin <phillip.morin@noaa.gov> | Erich Jarvis <ejarvis@rockefeller.edu> | Revive & Restore | ||||||||||||||
90 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenidae | Whales, dolphines, orcas | 54 | Eubalaena glacialis | North Atlantic right whale | 27606 | mEubGla1 | mEubGla1.hap2 | GCA_028564815.2 | GCF_028564815.1 | GCA_028564815.2 | Has X and Y | mEubGla1.hap1 | GCA_028571275.2 | MF409247.1 | Completed NCBI | SRX21609209 | HiFi, Hifiasm Hi-C phasing | 947 | 1,332 | 2,615,329,254 | M | Critically Endangered | Cetacean GP | Phil Morin <phillip.morin@noaa.gov> | Erich Jarvis <ejarvis@rockefeller.edu> | NOAA | |||||||||||||
91 | m32 | Mammals | Laurasiatheria | Cetartiodactyla (Cetacea) | Balaenidae | Whales, dolphines, orcas | 54 | Monodon monocero | narwhal | 40151 | mMonMon1 | mMonMon1.pri | GCA_005190385.3 | GCA_005190385.3 | (needs curation) | CLR I, FALCON unzip | 413 | 100 | 2,341,938,226 | M | Needs QC, curation, and possibly reassembly | Least Concern | Narwhal project | Camila Mazzoni <mazzoni@izw-berlin.de> | Harris Lewin <lewin@ucdavis.edu> | |||||||||||||||||||
92 | m33 | Mammals | Laurasiatheria | Cetartiodactyla (Hippopotamidae) | Hippopotamidae | Hippopotamuses | 54 | 2 | 1 | Hippopotamus amphibius | common hippopotamus | 9833 | 4 | mHipAmp2 | mHipAmp2.hap2 | GCA_030028045.1 | GCF_030028045.1 | GCF_030028045.1 | Has X only | mHipAmp2.hap1 | GCA_030028035.1 | AJ010957.1 | Completed NCBI | SRX1164570;SRX2880553;SRX5087252 | HiFi, Hifiasm Hi-C phasing | 356 | 582 | 2,538,242,855 | F | Vulnerable | VGP | Oliver Ryder <oryder@ucsd.edu> | Erich Jarvis <ejarvis@rockefeller.edu> | HHMI | ||||||||||
93 | m34 | Mammals | Laurasiatheria | Cetartiodactyla (Ruminantia) | Bovidae | Giraffes/Goats/Sheep/Deers/Cow | 60 | 231 | 8 | Ovis canadensis | bighorn sheep | 37174 | 5 | mOviCan1 | mOviCan1.pri | GCA_042477335.2 | GCF_042477335.2 | GCF_042477335.2 | Has X and Y | JN181255.1 | Completed NCBI | HiFi, ONT, Hi-C, Verkko | 44 | 41 | 2,974,267,070 | M | No BioSample page in NCBI? | Least Concern | Ruminant T2T | Tim Smith <tplsmith@gmail.com> | Ben Rosen <ben.rosen@usda.gov> | USDA | ||||||||||||
94 | m34 | Mammals | Laurasiatheria | Cetartiodactyla (Ruminantia) | Bovidae | Giraffes/Goats/Sheep/Deers/Cow | 60 | Ovis aries | domestic sheep | 9940 | mOviAri1 | mOviAri1.pri | GCA_040805955.1 | GCA_040805955.1 | Has X and Y | HiFi, ONT, Hi-C, HiFiasm trio | 28 | 28 | 2,853,626,077 | M | T2T genome | Not evaluated | Individual | Meng-Hua Li <menghua.li@cau.edu.cn> | Wei-Min Wang <wangweimin@lzu.edu.cn> | Biological Breeding-National Science and Technology Major Project | PMID: 39779954 | |||||||||||||||||
95 | m34 | Mammals | Laurasiatheria | Cetartiodactyla (Ruminantia) | Bovidae | Giraffes/Goats/Sheep/Deers/Cow | 60 | Bos taurus | Brahman cow | 9913 | UOA_Brahman_1 | mBosTauInd1.mat | GCA_003369695.2 | GCF_003369695.1 | GCA_003369695.2 | Has X only (create new assembly combo and move Y from pat) | mBosTauTau1.pat | GCA_003369685.2 | Completed NCBI | SRX21994536;SRX21994537;SRX21994538;SRX21994539;SRX21994540;SRX21994541;SRX21994542;SRX21994543;SRX21994544;SRX21994545 | RSII, TrioCanu | 1,712 | 1,435 | 2,580,764,822 | M | Should we substitute this new supposed T2T assembly, which is 0.6 Gb bigger GCA_043882115.1? Move Y from Angus to Brahman (Tim Smith & Adam Phillippy - new T@T? | Least Concern | Cattle | Tim Smith <tplsmith@gmail.com> | Adam Phillipy <adam.phillippy@nih.gov> | USDA | PMID: 30346939 | ||||||||||||
96 | m34 | Mammals | Laurasiatheria | Cetartiodactyla (Ruminantia) | Bovidae | Giraffes/Goats/Sheep/Deers/Cow | 60 | Cephalophula zebra | zebra duiker | 129233 | mCepZeb1 | Vulnerable | Colossal | Beth Shapiro <Beth Shapiro <beth.shapiro@gmail.com> | Erich Jarvis <ejarvis@rockefeller.edu> | Colossal | ||||||||||||||||||||||||||||
97 | m34 | Mammals | Laurasiatheria | Cetartiodactyla (Ruminantia) | Bovidae | Giraffes/Goats/Sheep/Deers/Cow | 60 | Capra hircus | goat | 9925 | mCapHir4 | mCapHir4.pri | GCA_041735815.1 | GCA_041735815.1 | Has X and Y | HiFi, ONT, HiFiasm trio | 31 | 31 | 2,863,923,675 | M | T2T genome | Least Concern | Individual | Meng-Hua Li <menghua.li@cau.edu.cn> | Zhi-Hong Liu <liuzh7799@163.com> | National Key Research and Development Program-Key Projects | PMID: 39567477 | |||||||||||||||||
98 | m34 | Mammals | Laurasiatheria | Cetartiodactyla (Ruminantia) | Cervidae | Giraffes/Goats/Sheep/Deers/Cow | 60 | Cervus elaphus | red deer | 9860 | mCerEla1 | mCerEla1.pri | GCA_910594005.1 | GCF_910594005.1 | GCF_910594005.1 | Has X only | mCerEla1.alt | GCA_910593805.1 | Completed NCBI | SRX1060418;SRX10954840;SRX10954841;SRX10954842;SRX12706344;SRX12706345;SRX12706346;SRX2880481 | HiFi, Hifiasm solo | 184 | 144 | 2,886,603,524 | F | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Josephin Pemberton <j.pemberton@ed.ac.uk> | Wellcome Trust | No PMID https://wellcomeopenresearch.org/articles/6-336 | |||||||||||||
99 | m34 | Mammals | Laurasiatheria | Cetartiodactyla (Ruminantia) | Cervidae | Giraffes/Goats/Sheep/Deers/Cow | 60 | Muntiacus reevesi | Reeves' muntjac | 9886 | mMunRee1 | mMunRee1.pri | GCA_963930625.1 | GCF_963930625.1 | GCF_963930625.1 | Has X only | mMunRee1.alt | GCA_963930665.1 | OZ005647.1 | Completed NCBI | HiFi, Hifiasm solo | 950 | 268 | 2,656,184,892 | F | Least Concern | DToL | Mark Blaxter <mb35@sanger.ac.uk> | Nick Ewart < nicholase@archipelago.ca.> | Wellcome Trust | PMID: 39345346 | |||||||||||||
100 | m34 | Mammals | Laurasiatheria | Cetartiodactyla (Ruminantia) | Cervidae | Giraffes/Goats/Sheep/Deers/Cow | 60 | Dama dama | fallow deer | 30532 | mDamDam1 | mDamDam1.mat | GCA_048126745.1 | GCA_048126745.1 | Has X (need to move Y into maternal haplotype) | mDamDam1.pat | GCA_048127045.1 | CM106757.1 | HiFi, Hifiasm Hi-C phasing | 1,450 | 1,303 | 2,723,309,090 | M | Has X (need to move Y into maternal haplotype) | Least Concern | Yggdrasil | Tom Gilbert <tgilbert@snm.ku.dk> | Sergei Kilver <sergei.kliver@sund.ku.dk> | Carlsberg Foundation, Colossal Biosciences, DNRF143 |