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A Comparative Genomics Multitool for Scientific Discovery and Conservation

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A Comparative Genomics Multitool for Scientific Discovery and Conservation Analysis https://doi.org/10.1038/s41586-020-2876-6 Supplementary information A comparative genomics multitool for scientific discovery and conservation In the format provided by the authors and unedited Nature | www.nature.com/nature Supplementary Table 1 Supplementary Table 1. Genome assembly statistics for all attemped and successful Zoonomia Project genomes. Of 173 species and subspecies initially planned for inclusion in the Zoonomia Project, genome assemblies have been generated and released for 132. For the remainder, acquisition of high quality samples was a major impediment. Set A: Discovar only genomes; Set B: Genomes upgraded to longer contiguity; Set C: Assembly failed; Set D: Sample failed QC; Set E: Sample not found; ** Genome assembly statistics output by DISCOVAR de novo. All samples were collected and shipped in compliance with the applicable regulations for sample collection, transfer, export and import. Contig Size (Gb; Mean Busco BUSCO Provider Provider Sequencing N50 (bp) Scaffold contigs base Complete Single BUSCO BUSCO BUSCO Set Species Common Name Order Family IUCN Biosample Institution contact location Genbank accession ** N50 (bp)** >1kb)** quality** Coverage** (n=4104) Copy Duplicated Fragmented Missing Liverpool Solenodon Hispaniolan School of Nicholas Uppsala A Eulipotyphla Solenodontidae Endangered SAMN07678062 GCA_004363575.1 244,273 422,311 2.05 35.8 29.3 90.4% 90.1% 0.3% 6.9% 2.7% paradoxus solenodon Tropical Casewell University Medicine Crocidura Indochinese University of Kevin Uppsala A Eulipotyphla Soricidae Least Concern SAMN07678044 GCA_004027635.1 8,485 8,747 2.23 33.4 32.2 20.6% 20.1% 0.5% 36.5% 42.9% indochinensis shrew Manitoba Campbell University Scalopus University of Kevin Uppsala A Eastern mole Eulipotyphla Talpidae Least Concern SAMN07678045 GCA_004024925.1 80,361 105,245 1.88 33.1 46.1 82.3% 81.9% 0.4% 13.0% 4.7% aquaticus Manitoba Campbell University Gracile shrew- University of Kevin Uppsala A Uropsilus gracilis Eulipotyphla Talpidae Least Concern SAMN07678046 GCA_004024945.1 50,461 64,331 1.88 33.9 54.2 65.1% 64.8% 0.3% 24.8% 10.1% like mole Manitoba Campbell University San Diego Oliver Uppsala A Vulpes lagopus Arctic fox Carnivora Canidae Least Concern SAMN07678118 GCA_004023825.1 88,551 123,667 2.32 35.8 36.8 81.5% 80.3% 1.2% 13.5% 5.0% Zoo Ryder University Canis lupus Domestic dog Cornell Adam Broad A Carnivora Canidae Least Concern SAMN07678141 GCA_004027395.1 110,028 173,941 2.34 33.6 66.5 85.0% 84.0% 1.0% 10.3% 4.7% familiaris (village dog) University Boyko Institute Cryptoprocta San Diego Oliver Broad A Fossa Carnivora Eupleridae Vulnerable SAMN07678074 GCA_004023885.1 137,953 186,904 2.32 32.2 46.3 85.9% 84.9% 1.0% 10.6% 3.5% ferox Zoo Ryder Institute Black-footed San Diego Oliver Broad A Felis nigripes Carnivora Felidae Vulnerable SAMN07678084 GCA_004023925.1 16,930 19,727 2.27 33.5 17.1 37.7% 37.5% 0.2% 40.8% 21.5% cat Zoo Ryder Institute Near San Diego Oliver Broad A Panthera onca Jaguar Carnivora Felidae SAMN07678103 GCA_004023805.1 66,276 123,177 2.37 33.2 60.7 78.4% 78.0% 0.4% 15.7% 5.9% threatened Zoo Ryder Institute Dwarf San Diego Oliver Uppsala A Helogale parvula Carnivora Herpestidae Least Concern SAMN07678086 GCA_004023845.1 116,675 184,757 2.33 34.0 32.3 83.9% 83.2% 0.7% 11.8% 4.3% mongoose Zoo Ryder University Suricata Zoo New Eric Broad A Meerkat Carnivora Herpestidae Least Concern SAMN07678040 GCA_004023905.1 156,832 196,874 2.36 34.1 46.9 86.1% 85.0% 1.1% 10.0% 3.9% suricatta England Baitchman Institute South African San Diego Oliver Uppsala A Mungos mungo banded Carnivora Herpestidae Least Concern SAMN07678097 GCA_004023785.1 189,084 247,492 2.35 35.9 46.7 87.4% 86.6% 0.8% 9.1% 3.5% Zoo Ryder University mongoose Near Smithsonian Klaus Broad A Hyaena hyaena Striped hyena Carnivora Hyaenidae SAMN07678047 GCA_004023945.1 53,836 69,191 2.34 32.7 31.3 71.1% 70.1% 1.0% 20.0% 8.9% threatened Insitute Koepfli Institute Western Smithsonian Klaus Uppsala A Spilogale gracilis Carnivora Mephitidae Least Concern SAMN07678050 GCA_004023965.1 66,417 90,418 2.33 33.1 33.2 76.7% 76.1% 0.6% 17.1% 6.2% spotted skunk Insitute Koepfli University Pteronura Smithsonian Klaus Broad A Giant otter Carnivora Mustelidae Endangered SAMN07678049 GCA_004024605.1 99,882 130,554 2.41 32.6 47.7 82.0% 81.4% 0.6% 13.3% 4.7% brasiliensis Insitute Koepfli Institute Mellivora San Diego Oliver Broad A Honey badger Carnivora Mustelidae Least Concern SAMN07678094 GCA_004024625.1 66,331 82,519 2.63 31.8 38.8 73.0% 72.1% 0.9% 18.5% 8.5% capensis Zoo Ryder Institute North Zalophus California sea Carolina Matthew Broad A Carnivora Otariidae Least Concern SAMN07678053 GCA_004024565.1 97,878 143,278 2.35 33.3 89.2 85.0% 83.3% 1.7% 10.3% 4.7% californianus lion State Breen Institute University Mirounga Northern Allyson Broad A Carnivora Phocidae Least Concern SAMN07678016 MGH/HMS GCA_004023865.1 54,778 67,070 2.31 32.3 35.6 72.3% 71.6% 0.7% 20.5% 7.2% angustirostris elephant seal Hindle Institute Paradoxurus Asian palm Smithsonian Klaus Broad A Carnivora Viverridae Least Concern SAMN07678048 GCA_004024585.1 67,775 77,417 2.32 33.1 36.9 74.8% 74.2% 0.6% 18.4% 6.8% hermaphroditus civet Insitute Koepfli Institute San Diego Oliver Broad A Manis tricuspis Tree pangolin Pholidota Manidae Vulnerable SAMN07678093 GCA_004765945.1 33,856 36,113 2.37 34.6 30.2 60.1% 59.5% 0.6% 27.2% 12.7% Zoo Ryder Institute Black Critically San Diego Oliver Broad A Diceros bicornis Perissodactyla Rhinocerotidae SAMN07678078 GCA_004027315.1 114,126 151,674 2.44 32.4 44.9 83.4% 82.9% 0.5% 12.9% 3.7% rhinocerous Endangered Zoo Ryder Institute Ceratotherium Northern white Critically San Diego Oliver Broad A Perissodactyla Rhinocerotidae SAMN07678069 GCA_004027795.1 23,748 25,821 2.40 32.9 29.2 48.7% 47.1% 1.6% 33.3% 18.0% simum cottoni rhino Endangered Zoo Ryder Institute San Diego Oliver Broad A Tapirus indicus Malayan tapir Perissodactyla Tapiridae Endangered SAMN07678113 GCA_004024905.1 234,383 320,013 2.33 34.4 41.4 84.1% 83.7% 0.4% 12.5% 3.4% Zoo Ryder Institute South San Diego Oliver Broad A Tapirus terrestris Perissodactyla Tapiridae Vulnerable SAMN07678114 GCA_004025025.1 184,442 207,300 2.34 44.0 44.2 82.0% 81.6% 0.4% 14.0% 4.0% American tapir Zoo Ryder Institute Antilocapra San Diego Oliver Broad A Pronghorn Cetartiodactyla Antilocapridae Least Concern SAMN07678063 GCA_004027515.1 75,180 90,528 2.41 32.5 49.3 80.4% 78.3% 2.1% 13.6% 6.0% americana Zoo Ryder Institute Southwest Eubalaena North Pacific Fisheries Phillip Broad A Cetartiodactyla Balaenidae Endangered SAMN07678124 GCA_004363455.1 41,990 48,127 2.31 33.7 40.0 69.0% 67.7% 1.3% 22.6% 8.4% japonica right whale Science Morin Institute Center Beatragus Critically San Diego Oliver Broad A Hirola Cetartiodactyla Bovidae SAMN07678065 GCA_004027495.1 60,436 72,932 2.55 34.6 23.1 76.6% 75.9% 0.7% 16.8% 6.6% hunteri Endangered Zoo Ryder Institute Hemitragus San Diego Oliver Broad A Nilgiri tahr Cetartiodactyla Bovidae Endangered SAMN07678087 GCA_004026825.1 69,919 89,641 2.58 32.5 29.4 79.9% 78.4% 1.5% 14.1% 6.0% hylocrius Zoo Ryder Institute Ovis canadensis Peninsular San Diego Oliver Broad A Cetartiodactyla Bovidae Endangered SAMN07678102 GCA_004026945.1 62,884 78,524 2.57 33.9 25.2 76.3% 75.2% 1.1% 17.0% 6.7% cremnobates bighorn sheep Zoo Ryder Institute Saiga tatarica Critically San Diego Oliver Broad A Russian saiga Cetartiodactyla Bovidae SAMN07678151 GCA_004024985.1 7,893 7,998 2.34 33.1 18.8 23.8% 23.2% 0.6% 42.4% 33.8% tatarica Endangered Zoo Ryder Institute Rangifer Siberian San Diego Oliver Uppsala A Cetartiodactyla Cervidae Vulnerable SAMN07678109 GCA_004026565.1 91,907 106,338 2.50 36.3 45.9 80.1% 77.8% 2.3% 13.1% 6.8% tarandus reindeer Zoo Ryder University Southwest Eschrichtius Fisheries Phillip Broad A Grey whale Cetartiodactyla Eschrichtiidae Least Concern SAMN07678123 GCA_004363415.1 78,871 107,875 2.33 32.3 40.5 79.2% 78.1% 1.1% 15.2% 5.6% robustus Science Morin Institute Center Hippopotamus San Diego Oliver Broad A Hippopotamus Cetartiodactyla Hippopotamidae Vulnerable SAMN07678089 GCA_004027065.1 84,845 98,945 2.39 33.9 77.0 80.8% 79.0% 1.8% 13.7% 5.5% amphibius Zoo Ryder Institute Southwest Amazon river Fisheries Phillip Broad A Inia geoffrensis Cetartiodactyla Iniidae Data deficient SAMN07678125 GCA_004363515.1 30,246 33,256 2.26 31.8 42.5 58.7% 57.8% 0.9% 25.3% 16.0% dolphin Science Morin Institute Center Southwest Pygmy sperm Fisheries Phillip Broad A Kogia breviceps Cetartiodactyla Kogiidae Data deficient SAMN07678126 GCA_004363705.1 31,609 34,952 2.37 34.5 38.8 58.8% 58.1% 0.7% 27.3% 13.9% whale Science Morin Institute Center Ocean Genome Monodon Broad A Narwhal Cetartiodactyla Monodontidae Least Concern SAMN07678023 Legacy/North Dan Distel GCA_004027045.1 78,802 99,265 2.31 33.2 34.7 76.1% 75.1% 1.0% 17.5% 6.4% monoceros Institute eastern University Ocean Monodon Genome Broad A monoceros Narwhal Cetartiodactyla Monodontidae Least Concern SAMN07678024 Legacy/North Dan Distel GCA_004026685.1 72,592 93,992 2.29 34.2 23.2 75.2% 74.2% 1.0% 17.7% 7.1% Institute (male) eastern University Moschus Siberian musk San Diego Oliver Broad A Cetartiodactyla Moschidae Vulnerable SAMN07678096 GCA_004024705.1 39,944 54,975 2.62 34.1 64.9 73.2% 71.6% 1.6% 18.7% 8.1% moschiferus deer Zoo Ryder Institute The Museum Phocoena Harbor of Vertebrate Michael Broad A Cetartiodactyla Phocoenidae Least Concern SAMN07678060 GCA_004363495.1 105,655 138,932 2.32 34.5 56.4 80.9% 79.8% 1.1% 13.0% 6.1% phocoena porpoise Zoology at Nachman Institute Berkeley Southwest Platanista Indus river Fisheries Phillip Broad A Cetartiodactyla Platanistidae Endangered SAMN07678149 GCA_004363435.1 23,592 27,013 2.36 34.1 28.0 49.7% 48.5% 1.2% 34.6% 15.7% gangetica minor dolphin Science Morin Institute Center Supplementary Table 1 Supplementary Table 1.
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