TY - JOUR
T1 - A comparative genomics multitool for scientific discovery and conservation
AU - Zoonomia Consortium
AU - Genereux, Diane P.
AU - Serres, Aitor
AU - Armstrong, Joel
AU - Johnson, Jeremy
AU - Marinescu, Voichita D.
AU - Murén, Eva
AU - Juan, David
AU - Bejerano, Gill
AU - Casewell, Nicholas R.
AU - Chemnick, Leona G.
AU - Damas, Joana
AU - Di Palma, Federica
AU - Diekhans, Mark
AU - Fiddes, Ian T.
AU - Garber, Manuel
AU - Gladyshev, Vadim N.
AU - Goodman, Linda
AU - Haerty, Wilfried
AU - Houck, Marlys L.
AU - Hubley, Robert
AU - Kivioja, Teemu
AU - Koepfli, Klaus Peter
AU - Kuderna, Lukas F.K.
AU - Lander, Eric S.
AU - Meadows, Jennifer R.S.
AU - Murphy, William J.
AU - Nash, Will
AU - Noh, Hyun Ji
AU - Nweeia, Martin
AU - Pfenning, Andreas R.
AU - Pollard, Katherine S.
AU - Ray, David A.
AU - Shapiro, Beth
AU - Smit, Arian F.A.
AU - Springer, Mark S.
AU - Steiner, Cynthia C.
AU - Swofford, Ross
AU - Taipale, Jussi
AU - Teeling, Emma C.
AU - Turner-Maier, Jason
AU - Alfoldi, Jessica
AU - Birren, Bruce
AU - Ryder, Oliver A.
AU - Lewin, Harris A.
AU - Paten, Benedict
AU - Marques-Bonet, Tomas
AU - Lindblad-Toh, Kerstin
AU - Karlsson, Elinor K.
N1 - Funding Information:
Acknowledgements We thank the many individuals who provided samples and advice, including C. Adenyo, C. Avila, E. Baitchman, R. Behringer, A. Boyko, M. Breen, K. Campbell, P. Campbell, C. J. Conroy, K. Cooper, L. M. Dávalos, F. Delsuc, D. Distel, C. A. Emerling, J. Fronczek, N. Gemmel, J. Good, K. He, K. Helgen, A. Hindle, H. Hoekstra, R. Honeycutt, P. Hulva, W. Israelsen, B. Kayang, R. Kennerley, M. Korody, D. N. Lee, E. Louis, M. MacManes, A. Misuraca, A. Mitelberg, P. Morin, A. Mouton, M. Murayama, M. Nachman, A. Navarro, R. Ogden, B. Pasch, S. Puechmaille, T. J. Robinson, S. Rossiter, M. Ruedi, A. Seifert, S. Thomas, S. Turvey, G. Verbeylen and the late R. J. Baker. We also thank the Broad Institute Genomics Platform and SNP & SEQ Technology Platform (part of the National Genomics Infrastructure (NGI) Sweden and Science for Life Laboratory) and Swedish National Infrastructure for Computing (SNIC) at Uppmax. This project was funded by NIH NHGRI R01HG008742 (E.K.K., B.B., D.P.G., R.S., J.T.-M., J.J., H.J.N., B.P. and J. Armstrong), Swedish Research Council Distinguished Professor Award (K.L.-T., V.D.M., E.M. and J.R.S.M.), Swedish Research Council grant 2018-05973 (K.L.-T.), Knut and Alice Wallenberg Foundation (K.L.-T., V.D.M., E.M. and J.R.S.M.), Uppsala University (K.L.-T., V.D.M., E.M., J.R.S.M., J.J., J. Alfoldi and L.G.), Broad Institute Next10 (L.G.), Gladstone Institutes (K.S.P.), NIH NHGRI 5R01HG002939 (A.F.A.S. and R.H.), NIH NHGRI 5U24HG010136 (A.F.A.S. and R.H.), NIH NHGRI 5R01HG010485 (B.P. and M.D.), NIH NHGRI 2U41HG007234 (B.P., M.D. and J. Armstrong), NIH NIA 5PO1AG047200 (V.N.G.), NIH NIA 1UH2AG064706 (V.N.G.), BFU2017-86471-P MINECO/FEDER, UE (T.M.-B.), Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya GRC 2017 SGR 880 (T.M.-B.), Howard Hughes International Early Career (T.M.-B.), European Research Council Horizon 2020 no. 864203 (T.M.-B.), Obra Social ‘La Caixa’ (T.M.-B.), BBSRC BBS/E/T/000PR9818, BBS/E/T/ 000PR9783 (W.H. and W.N.), BBSRC Core Strategic Programme Grant BB/P016774/1 (W.H., W.N. and F.D.), Sir Henry Dale Fellowship 200517/Z/16/Z jointly funded by the Wellcome Trust and the Royal Society (N.R.C.), FJCI-2016-29558 MICINN (D.J.), Prince Albert II Foundation of Monaco and Canada, Global Genome Initiative, Smithsonian Institution (M.N.), European Research Council Research Grant ERC-2012-StG311000 (E.C.T.), Irish Research Council Laureate Award (E.C.T.), UK Medical Research Council MR/P026028/1 (W.H. and W.N.), National Science Foundation DEB-1457735 (M.S.S.), National Science Foundation DEB-1753760 (W.J.M.), National Science Foundation IOS-2029774 (E.K.K. and D.P.G.), Robert and Rosabel Osborne Endowment (H.A.L. and J.D.), Swedish Research Council, FORMAS 221-2012-1531 (J.R.S.M.), NSF RoL: FELS: EAGER: DEB 1838283 (D.A.R.) and Academy of Finland grant to Center of Excellence in Tumor Genetics Research no. 312042 (T.K. and J.T.).
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/11/12
Y1 - 2020/11/12
N2 - The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
AB - The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
UR - http://www.scopus.com/inward/record.url?scp=85079408349&partnerID=8YFLogxK
U2 - 10.1038/s41586-020-2876-6
DO - 10.1038/s41586-020-2876-6
M3 - Article
C2 - 33177664
AN - SCOPUS:85079408349
VL - 587
SP - 240
EP - 245
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7833
ER -