The Vertebrate Genomes Project Phase I: A global reference genome resource

作者：Giulio Formenti, Dominic Absolon, Linelle Abueg, F.J. Ackerman, Farooq O. Al-Ajli, Alexandre Luis Padovan Aleixo, Agostinho Antunes, Dahiana Arcila, Jean‐Nicolas Audet, Jennifer Balacco, Alan J. S. Beavan, Katherine Belov, Ricardo Betancur‐R, Shelby Bidwell, Matthew T. Biegler, Iliana Bista, Mark Blaxter, Kevin Boyer, Ingo Braasch, Ian Bradbury, Nadolina Brajuka, Anne M. Bronikowski, Tom Brown, George B. Butler, Shuo Cao, Eduardo Charvel, Ying Chen, Claúdio Ciofi, Hiram Clawson, Joanna Collins, Solenne Correard, Shannon Corrigan, Mélanie Couture, Andrew J. Crawford, Nathalia D.R. D'Alessandre, Helena B. Conceição, Rute R. da Fonseca, Minoli Daigavane, Jeronymo Dalapicolla, Mark de Bruyn, Emma de Jong, Diego De Panis, H. William Detrich, C Scott, Mark Diekhans, Erick Duarte, Richard Durbin, Merly Escalona, Michel Eschenbrenner, Olivier Fédrigo, Jonathan Fenn, Patrick Flannery, Niamh Forde, Simone M. Gable, Pedro A. F. Galante, Rajee Ganesan, Amanda M. Gardiner, Erik Garrison, Neil J. Gemmell, M. Thomas P. Gilbert, François Giudicelli, Tássia Mangetti Gonçalves, Gabriela D. A. Guardia, Andrea Guarracino, Anshu Gupta, Bettina Haase, Delson Hays, Glenn Hickey, Michael Hiller, Paul M. Hime, Carolyn J. Hogg, Kathleen L. Horan, Kerstin Howe, Daniel 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 Kovačić, Ksenia Krasheninnikova, Lukas F. K. Kuderna, Ryan A. Langlois, Delphine Larivière, Denis M. Larkin, Chul Lee, Young Ho Lee, Harris A. Lewin, Daven Lim, Runyang Nicolas Lou, Sarah S. T. Mak, Kateryna D. Makova, Laia Marín-Gual, Tomàs Marquès‐Bonet, Fergal J. Martin, Thomas C. Mathers, Camila J. Mazzoni, Kirsty McCaffrey, Shane McCarthy, Jack A Medico, Rafael L. V. Mercuri, Axel Meyer, Pawel Michalak, Siavash Mirarab, Phillip A. Morin, Jacquelyn Mountcastle, Robert W. Murphy, Terence D. Murphy, Eugene W. Myers, Gavin J. P. Naylor, Thomas Near, Anton Nekrutenko, Zemin Ning, Ben J. Novak, Michelle F O'Brien, Mary J. O’Connell, Brian P O'Toole, Sadye Paez, Benedict Paten, Michael Paulini, Sarah Pelan, Matthew W. Pennell, Andreas R. Pfenning, Adam M. Phillippy, Brendan J. Pinto, Martin Pippel, M. 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 Steiner, Peter H. Sudmant, Deacon Sweeney, Samuel C Talbot, Christopher H. Taylor, Emma C. Teeling, Françoise Thibaud‐Nissen, Tatiana Tilley, Nataliya Timoshevskaya, Patrick Traore, Yatish Turakhia, Marcela Uliano‐Silva, Chris Venditti, Byrappa Venkatesh, Sonja C. Vernes, Wesley C. Warren, Conor Whelan, Melissa A. Wilson, Sylke Winkler, Jonathan Wood, Guojie Zhang, Guoyan Zhao, Erich D Jarvis · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2026 · DOI：10.64898/2026.06.24.732306 · 被引用次数：4 · 研究领域：Genomics and Phylogenetic Studies、Chromosomal and Genetic Variations、Genome Rearrangement Algorithms

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. 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 ∼97% of vertebrate orders, along with additional lineages within those orders, totaling 815 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 methods, alongside the growth of associated consortium initiatives and international collaborations. 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 ...