Kavli Affiliate: Erich Jarvis
| Authors: Giulio Formenti, Dominic E. Absolon, Linelle Ann L. Abueg, Francine Ackerman, Farooq Omar Al-Ajli, Alexandre Aleixo, Agostinho Antunes, Dahiana Arcila, Jean-Nicolas Audet, Jennifer R. Balacco, Alan James Stephen Beavan, Katherine Belov, Ricardo Betancur-R., Shelby L Bidwell, Matthew T Biegler, Iliana Bista, Mark Blaxter, Kevin Boyer, Ingo Braasch, Ian R Bradbury, Nadolina Brajuka, Anne M Bronikowski, Tom Brown, George Butler, Shuo Cao, Eduardo Charvel, Ying Chen, Claudio Ciofi, Hiram M. Clawson, Joanna Clare Collins, Solenne Correard, Shannon Corrigan, Melanie Couture, Andrew J. Crawford, Nathalia D.R. D’Alessandre, Helena B. da Conceicao, Rute R da Fonseca, Minoli Daigavane, Jeronymo Dalapicolla, Mark de Bruyn, Emma de Jong, Diego N De Panis, H. William Detrich III, Carol DeWeese Scott, Mark Diekhans, Erick Duarte, Richard Durbin, Merly Escalona, Michel Eschenbrenner, Olivier Fedrigo, Jonathan Fenn, Patrick Flannery, Niamh Forde, Simone M Gable, Pedro AF Galante, Rajee Ganesan, Amanda Gardiner, Erik Garrison, Neil J Gemmell, M Thomas P Gilbert, Francois Giudicelli, Tassia Mangetti Goncalves, Gabriela Der Agopian Guardia, Andrea Guarracino, Anshu Gupta, Bettina Haase, Delson Hays, Glenn Hickey, Michael Hiller, Paul M Hime, Carolyn J Hogg, Kathleen M Horan, Kerstin Howe, Danny Jackson, Nivesh Jain, Lin Kang, Sergei Kliver, Byung June Ko, Klaus-Peter Koepfli, Aleksey Komissarov, Lisa M Komoroske, Bonhwang Koo, Sergey Koren, Jonas Korlach, Iva Kovacic, Ksenia Krasheninnikova, Lukas FK Kuderna, Ryan A Langlois, Delphine Lariviere, Denis M Larkin, Chul Lee, Young Ho Lee, Harris A Lewin, Daven Lim, Runyang Nicolas Lou, Sarah ST Mak, Kateryna D Makova, Laia Marin-Gual, Tomas Marques-Bonet, Fergal James Martin, Thomas C Mathers, Camila J Mazzoni, Kirsty McCaffrey, Shane A McCarthy, Jack A Medico, Rafa el Luiz Vieira Mercuri, Axel Meyer, Pawel Michalak, Siavash Mirarab, Phillip A Morin, Jacquelyn Mountcastle, Robert W Murphy, Terence D Murphy, Eugene W Myers, Gavin JP Naylor, Thomas Near, Anton Nekrutenko, Zemin Ning, Ben J Novak, Michelle F O’Brien, Mary Josephine O’Connell, Brian P O’Toole, Sadye Paez, Benedict Paten, Michael Paulini, Sarah E Pelan, Matt Pennell, Andreas R Pfenning, Adam M Phillippy, Brendan Pinto, Martin Pippel, Marina Popova, Maksym Prylutskyi, Arang Rhie, Hugues Roest Crollius, Aurora Ruiz-Herrera, Oliver Ryder, Yana Safonova, Camilla A Santos, Michael C Schatz, Simona Secomandi, H. Bradley Shaffer, Lauren Shalmiyev, Beth Shapiro, Jeramiah J Smith, Marco Sollitto, Cibele G Sotero-Caio, Cynthia Cristina Steiner, Peter H Sudmant, Deacon J Sweeney, Samuel C Talbot, Christopher H Taylor, Emma C Teeling, Francoise Thibaud-Nissen, Tatiana Tilley, Nataliya Timoshevskaya, Patrick Traore, Yatish Turakhia, Marcela Uliano-Silva, Chris Venditti, Byrappa Venkatesh , Sonja C Vernes, Wesley C Warren, Conor V Whelan, Melissa A Wilson, Sylke Winkler, Jonathan MD Wood, Guojie Zhang, Guoyan Zhao, Erich D Jarvis and VertebrateGenomes Project Consortium Phase I
| Summary:
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 lineages within those orders, totaling 816 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods2–4, alongside the growth of associated consortium initiatives and international collaborations5–9. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers a reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine.