Peer-Reviewed Publication
bioRxiv2026June 25, 2026Journal Article
The Vertebrate Genomes Project Phase I: A global reference genome resource.
Giulio Formenti1, Dominic E Absolon2, Linelle Ann L Abueg1, Francine Ackerman1, Farooq O Al-Ajli1,3,4, Alexandre Aleixo5, Agostinho Antunes6,7, Dahiana Arcila8, Jean-Nicolas Audet9,10,11, Jennifer R Balacco1, Alan J S Beavan12,13, Katherine Belov14,15, Ricardo Betancur-R8, Shelby L Bidwell16, Matthew T Biegler10, Iliana Bista2,17, Mark Blaxter2, Kevin Boyer18, Ingo Braasch19, Ian R Bradbury20, Nadolina Brajuka1, Anne M Bronikowski19,21, Tom Brown22,23, George Butler24,25, Shuo Cao26, Eduardo Charvel27, Ying Chen1, Claudio Ciofi28, Hiram M Clawson29, Joanna C Collins2, Solenne Correard30,31, Shannon Corrigan32,33, Mélanie Couture1,9, Andrew J Crawford34, Nathália D D'Alessandre35, Helena B da Conceicao35,36, Rute R da Fonseca6,37, Minoli Daigavane38, Jeronymo Dalapicolla5,39, Mark de Bruyn40, Emma de Jong32, Diego N De Panis23,41, H William Detrich42, Carol DeWeese Scott16, Mark Diekhans29, Erick Duarte1, Richard Durbin2,43, Merly Escalona44,45, Michel Eschenbrenner16, Olivier Fedrigo1, Jonathan Fenn12,13, Patrick Flannery1, Niamh Forde46, Simone M Gable47, Pedro A Galante35, Rajee Ganesan48, Amanda Gardiner43, Erik Garrison26, Neil J Gemmell49,50, M Thomas P Gilbert51,52, François Giudicelli53, Tássia M Gonçalves18, Gabriela D A Guardia35, Andrea Guarracino54, Anshu Gupta55, Bettina Haase1, Delson Hays8, Glenn Hickey29, Michael Hiller56,57, Paul M Hime18,58, Carolyn J Hogg14,15, Kathleen M Horan1, Kerstin Howe2, Danny Jackson59, Nivesh Jain1, Lin Kang60,61,62, Sergei Kliver51, Byung June Ko63, Klaus-Peter Koepfli64, Aleksey Komissarov65, Lisa M Komoroske66, Bonhwang Koo1, Sergey Koren67, Jonas Korlach68, Iva Kovacic69, Ksenia Krasheninnikova2, Lukas F Kuderna70, Ryan A Langlois71, Delphine Lariviere72, Denis M Larkin73, Chul Lee10, Young Ho Lee74, Harris A Lewin47,75, Daven Lim76,77, Runyang Nicolas Lou76, Sarah S Mak51, Kateryna D Makova63, Laia Marín-Gual78,79, Tomas Marques-Bonet80,81,82,83, Fergal J Martin2, Thomas C Mathers2, Camila J Mazzoni23,84, Kirsty McCaffrey1, Shane A McCarthy2, Jack A Medico1, Rafael L V Mercuri35, Axel Meyer85,86,87, Pawel Michalak60,61,88, Siavash Mirarab89, Phillip A Morin90, Jacquelyn Mountcastle1, Robert W Murphy91,92, Terence D Murphy16, Eugene W Myers22,93, Gavin J Naylor94, Thomas Near95,96, Anton Nekrutenko72, Zemin Ning2, Ben J Novak97, Michelle F O'Brien98, Mary J O'Connell12,13,99, Brian P O'Toole1, Sadye Paez10, Benedict Paten29, Michael Paulini2, Sarah E Pelan2, Matt Pennell100, Andreas R Pfenning48,101, Adam M Phillippy67,102,103,104, Brendan Pinto105,106, Martin Pippel107, Marina Popova108, Maksym Prylutskyi73, Arang Rhie67, Hugues Roest Crollius53, Aurora Ruiz-Herrera78,79, Oliver Ryder109, Yana Safonova110,111, Camilla A Santos2, Michael C Schatz102,112, Simona Secomandi1,10, H B Shaffer113,114, Lauren Shalmiyev1, Beth Shapiro115, Jeramiah J Smith116,117, Marco Sollitto1,28, Cibele G Sotero-Caio2, Cynthia C Steiner109, Peter H Sudmant76, Deacon J Sweeney16, Samuel C Talbot1,118, Christopher H Taylor12,13, Emma C Teeling2,119, Françoise Thibaud-Nissen16, Tatiana Tilley1, Nataliya Timoshevskaya116,120, Patrick Traore1, Yatish Turakhia89, Marcela Uliano-Silva2,121, Chris Venditti122, Byrappa Venkatesh123, Sonja C Vernes124, Wesley C Warren125,126, Conor V Whelan1, Melissa A Wilson59, Sylke Winkler22,127, Jonathan M Wood2, Guojie Zhang128,129, Guoyan Zhao18,130,131, Erich D Jarvis1,9,10,
1Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
2Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
3Katara Biodiversity Genomes Program, Katara Cultural Village Foundation, Doha, Qatar.
4Sidra Medicine, Doha, Qatar.
5Vale Institute of Technology, Belém, Pará 66055-090, Brazil.
6CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal.
7Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal.
8Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA.
9Rockefeller University Field Research Center, Millbrook, NY 12585, USA.
10Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA.
11Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
12Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK.
13Computational and Molecular Evolutionary Biology Group, School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham NG7 2UH, UK.
14School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, 2006, Australia.
15ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, 2006, Australia.
16National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
17Senckenberg Research Institute and Natural History Museum, 60325 Frankfurt am Main, Germany.
18Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
19Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.
20Fisheries and Oceans Canada, St. John's, Newfoundland A1A 5J, Canada.
21Dept of Ecology, Evolution, Organismal Biology, Iowa State University, Ames, IA 50010, USA.
22Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), 01307 Dresden, Germany.
23Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany.
24University College London Cancer Institute, University College London, London WC1E 6DD, UK.
25The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
26Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
27Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, CA 92093, USA.
28Department of Biology, University of Florence, Sesto Fiorentino 50019, Italy.
29UC Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA.
30GenOuest, Univ Rennes, INRIA, CNRS, IRISA, 35000 Rennes, France.
31IGEPP, INRAE, Institut Agro, University of Rennes, 35000 Rennes, France.
32Minderoo OceanOmics Centre at UWA, UWA Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia.
33Minderoo Foundation, Nedlands, Western Australia 6000, Australia.
34Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia.
35Centro de Oncologia Molecular, Hospital Sirio-Libanes, São Paulo, São Paulo, 01308-060, Brazil.
36Boston Children's Hospital, Boston, MA 02115, USA.
37Center for Global Mountain Biodiversity, The Globe Institute, University of Copenhagen, 1165 Copenhagen, Denmark.
38Yale University, New Haven, CT 06511, USA.
39Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, 58051-900, Brazil.
40Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland 4111, Australia.
41Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany.
42Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, MA 01908, USA.
43Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
44Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
45Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
46Center for Reproductive Health, School of Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK.
47Global Futures Laboratory, Arizona State University, Phoenix, AZ 85281, USA.
48Ray and Stephanie Lane Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
49Department of Anatomy, Faculty of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.
50Genomics Aotearoa, University of Otago, Dunedin 9054, New Zealand.
51Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark.
52University Museum, NTNU, 7012 Trondheim, Norway.
53Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.
54Bioinnovation and Genome Sciences, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA.
55Department of Computer Science and Engineering, UC San Diego, La Jolla, CA 92093, USA.
56Senckenberg - Leibniz Institution for Biodiversity and Earth System Research, 60325 Frankfurt am Main, Germany.
57Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
58McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
59Comparative Genomics and Reproductive Health Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
60Division of Biomedical Affairs & Research, Edward Via College of Osteopathic Medicine, Monroe, LA 71203, USA.
61Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA 24060, USA.
62College of Pharmacy, University of Louisiana Monroe, Monroe, LA 71203, USA.
63Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
64College of Science, George Mason University, Fairfax, VA 22030, USA.
65Neapolis University Pafos, Paphos, 8042, Cyprus.
66Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA.
67Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
68Pacific Biosciences, Menlo Park, CA 94025, USA.
69University of Copenhagen, Faculty of Science, 2100 Copenhagen, Denmark.
70Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA 92122, USA.
71University of Minnesota, Minneapolis, MN 55455, USA.
72Department of Biochemistry and Molecular Biology (BMB), Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA.
73Royal Veterinary College, University of London, London, NW1 0TU, UK.
74Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea.
75Department of Evolution and Ecology, University of California, Davis, Davis, CA, 95616, USA.
76Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
77ETH Zürich, 8092 Zürich, Switzerland.
78Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain.
79Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain.
80Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.
81Institute of Evolutionary Biology (UPF-CSIC) and Center of Genomic Regulation (CRG), PRBB, 08003 Barcelona, Spain.
82CNAG, Centro Nacional de Analisis Genomico, 08028 Barcelona, Spain.
83Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.
84Berlin Center for Genomics in Biodiversity Research (BeGenDiv), 14195 Berlin, Germany.
85Department of Biology, University of Konstanz, 78462 Konstanz, Germany.
86MOE Key Laboratory of Freshwater Fish Reproduction and Development, College of Fisheries, School of Life Sciences, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Southwest University, Chongqing 400038, China.
87Marine Biodiversity and Ecological Evolution Research Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
88Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 3498838, Israel.
89Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
90Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA 92037, USA.
91Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 1A1, Canada.
92Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada.
93Okinawa Institute of Science and Technology, Okinawa 904-0412, Japan.
94Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
95Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.
96Yale Peabody Museum, New Haven, CT 06511, USA.
97Revive & Restore, Sausalito, CA 94965, USA.
98WWT, Gloucestershire GL2 7BT, UK.
99The Natural History Museum, London, London SW7 5BD, UK.
100Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA.
101Neuroscience Institute - Carnegie Mellon University, Pittsburgh PA, 15213, USA.
102Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
103Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
104Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
105Center for Evolution & Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
106Department of Zoology, Milwaukee Public Museum, Milwaukee, WI 53233, USA.
107Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, 752 37 Uppsala, Sweden.
108The Center for Bio- and Medical Technologies, Moscow, Russia.
109Conservation Science, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.
110Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA.
111Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
112Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
113Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
114La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA.
115Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
116Department of Biology, University of Kentucky, Lexington, KY 40508, USA.
117Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA.
118Center for Quantitative Life Sciences, Oregon State University, Corvallis, OR 97331, USA.
119School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
120Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY 40508, USA.
121Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway.
122School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
123Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
124School of Biology, The University of St Andrews, St. Andrews KY16 9AJ, UK.
125Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
126Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65211, USA.
127DRESDEN-concept Genome Center, 01307 Dresden, Germany.
128Center of Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
129Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China.
130Department of Neurology, Washington University School of Medicine, St. Louis, MO 63108, USA.
131Hope Center for Neurological Disorders and Charles F. and Joanne Knight Alzheimer's Disease Research Center, St. Louis, MO 63108, USA.
Abstract
The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ~70,000 extant vertebrate species1. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for ~95% of vertebrate orders, along with additional lineage…
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