1. A comparative genomics multitool for scientific discovery and conservation
- Author
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Oliver A. Ryder, Jeremy Johnson, Ross Swofford, Wilfried Haerty, Jennifer R. S. Meadows, Gill Bejerano, Eva Murén, Jessica Alföldi, Marlys L. Houck, Katherine S. Pollard, David A. Ray, Emma C. Teeling, Robert Hubley, Leona G. Chemnick, Eric S. Lander, Vadim N. Gladyshev, Martin T. Nweeia, Federica Di Palma, Teemu Kivioja, Voichita D. Marinescu, Hyun Ji Noh, Joana Damas, Mark Diekhans, Mark S. Springer, Arian F.A. Smit, Nicholas R. Casewell, Benedict Paten, Lukas F. K. Kuderna, Manuel Garber, Bruce W. Birren, Joel Armstrong, Tomas Marques-Bonet, Aitor Serres, Jason Turner-Maier, Diane P. Genereux, Ian T. Fiddes, Elinor K. Karlsson, William J. Murphy, Will Nash, David Juan, Harris A. Lewin, Cynthia C. Steiner, Kerstin Lindblad-Toh, Linda Goodman, Andreas R. Pfenning, Beth Shapiro, Klaus-Peter Koepfli, Jussi Taipale, National Institutes of Health (US), Swedish Research Council, Knut and Alice Wallenberg Foundation, Uppsala University, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Howard Hughes Medical Institute, European Research Council, Fundación 'la Caixa', Wellcome Trust, Royal Society (UK), Ministerio de Economía y Competitividad (España), Fondation Prince Albert II de Monaco, Smithsonian Institution, Irish Research Council, Medical Research Council (UK), National Science Foundation (US), Academy of Finland, Research Programs Unit, ATG - Applied Tumor Genomics, University of Helsinki, Department of Pathology, Jussi Taipale / Principal Investigator, Armstrong, Joel [0000-0003-2077-4671], Juan, David [0000-0003-1912-9667], Bejerano, Gill [0000-0001-5179-3635], Casewell, Nicholas R. [0000-0002-8035-4719], Garber, Manuel [0000-0001-8732-1293], Kivioja, Teemu [0000-0002-7732-2177], Kuderna, Lukas F. K. [0000-0002-9992-9295], Lander, Eric S. [0000-0003-2662-4631], Noh, Hyun Ji [0000-0002-6634-0599], Nweeia, Martin [0000-0001-7079-4123], Pfenning, Andreas R. [0000-0002-3447-9801], Pollard, Katherine S. [0000-0002-9870-6196], Shapiro, Beth [0000-0002-2733-7776], Teeling, Emma C. [0000-0002-3309-1346], Alfoldi, Jessica [0000-0001-9713-6200], Ryder, Oliver A. [0000-0003-2427-763X], Lewin, Harris A. [0000-0002-1043-7287], Paten, Benedict [0000-0001-8863-3539], Marques-Bonet, Tomas [0000-0002-5597-3075], Karlsson, Elinor K. [0000-0002-4343-3776], and Apollo - University of Cambridge Repository
- Subjects
0106 biological sciences ,Biomedical Research ,Zoonomia Consortium ,Loss of Heterozygosity ,Genome informatics ,01 natural sciences ,Evolutionsbiologi ,Neoplasms ,HISTORY ,Glucose homeostasis ,Phylogeny ,0303 health sciences ,Multidisciplinary ,BROWN ADIPOSE-TISSUE ,Eutheria ,ALGORITHMS ,1184 Genetics, developmental biology, physiology ,Ecological genetics ,Genomics ,Biodiversity ,Extinction ,Knowledge Discovery ,Phylogenetics ,EXTINCTION ,Biotechnology ,Conservation of Natural Resources ,Medicina -- Investigació ,Life on Land ,Evolution ,Genetic Speciation ,General Science & Technology ,Scientific discovery ,Computational biology ,Biology ,Extinction, Biological ,Infections ,010603 evolutionary biology ,Descobriments científics ,Risk Assessment ,Evolutionary genetics ,Evolution, Molecular ,03 medical and health sciences ,Species Specificity ,Genetic ,Genetics ,Animals ,Humans ,Selection, Genetic ,Genetik ,Selection ,030304 developmental biology ,Comparative genomics ,Evolutionary Biology ,Human evolutionary genetics ,Venoms ,Human Genome ,Molecular ,Genetic Variation ,15. Life on land ,FRAMEWORK ,Biological ,Genòmica ,Biodiversitat -- Conservació ,GLUCOSE-HOMEOSTASIS ,Sequence Alignment ,human activities ,Mamífers ,Analysis - Abstract
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., 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.).
- Published
- 2020