Towards complete and error-free genome assemblies of all vertebrate species

Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher N. Balakrishnan, Dave Burt, Julia M. George, Matthew T. Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich, Hannes Svardal, Maximilian Wagner, Gavin J. P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E. Dagnew, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio V. Mello, Samantha R. Friedrich, Peter V. Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H. S. Kraus, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Palma, Tomas Marques-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Haussler, Stephen J. O’Brien, Jonas Korlach, Harris A. Lewin, Kerstin Howe (), Eugene W. Myers (), Richard Durbin (), Adam M. Phillippy () and Erich D. Jarvis ()
Additional contact information
Arang Rhie: National Human Genome Research Institute, National Institutes of Health
Shane A. McCarthy: University of Cambridge
Olivier Fedrigo: The Rockefeller University
Joana Damas: University of California Davis
Giulio Formenti: The Rockefeller University
Sergey Koren: National Human Genome Research Institute, National Institutes of Health
Marcela Uliano-Silva: Department of Evolutionary Genetics
William Chow: Wellcome Sanger Institute
Arkarachai Fungtammasan: DNAnexus Inc.
Juwan Kim: Seoul National University
Chul Lee: Seoul National University
Byung June Ko: Seoul National University
Mark Chaisson: University of Southern California
Gregory L. Gedman: The Rockefeller University
Lindsey J. Cantin: The Rockefeller University
Francoise Thibaud-Nissen: National Library of Medicine, NIH
Leanne Haggerty: Wellcome Genome Campus
Iliana Bista: University of Cambridge
Michelle Smith: Wellcome Sanger Institute
Bettina Haase: The Rockefeller University
Jacquelyn Mountcastle: The Rockefeller University
Sylke Winkler: Max Planck Institute of Molecular Cell Biology and Genetics
Sadye Paez: The Rockefeller University
Jason Howard: Novogene
Sonja C. Vernes: Max Planck Institute for Psycholinguistics
Tanya M. Lama: University of Massachusetts Cooperative Fish and Wildlife Research Unit
Frank Grutzner: University of Adelaide
Wesley C. Warren: University of Missouri
Christopher N. Balakrishnan: East Carolina University
Dave Burt: University of Queensland
Julia M. George: Clemson University
Matthew T. Biegler: The Rockefeller University
David Iorns: The Genetic Rescue Foundation
Andrew Digby: Kākāpō Recovery, Department of Conservation
Daryl Eason: Kākāpō Recovery, Department of Conservation
Bruce Robertson: University of Otago
Taylor Edwards: University of Arizona Genetics Core
Mark Wilkinson: Natural History Museum
George Turner: Bangor University
Axel Meyer: University of Konstanz
Andreas F. Kautt: University of Konstanz
Paolo Franchini: University of Konstanz
H. William Detrich: Northeastern University Marine Science Center
Hannes Svardal: University of Antwerp
Maximilian Wagner: Karl-Franzens University of Graz
Gavin J. P. Naylor: University of Florida
Martin Pippel: Max Planck Institute of Molecular Cell Biology and Genetics
Milan Malinsky: Wellcome Sanger Institute
Mark Mooney: Tag.bio
Maria Simbirsky: DNAnexus Inc.
Brett T. Hannigan: DNAnexus Inc.
Trevor Pesout: University of California
Marlys Houck: San Diego Zoo Global
Ann Misuraca: San Diego Zoo Global
Sarah B. Kingan: Pacific Biosciences
Richard Hall: Pacific Biosciences
Zev Kronenberg: Pacific Biosciences
Ivan Sović: Pacific Biosciences
Christopher Dunn: Pacific Biosciences
Zemin Ning: Wellcome Sanger Institute
Alex Hastie: Bionano Genomics
Joyce Lee: Bionano Genomics
Siddarth Selvaraj: Arima Genomics
Richard E. Green: University of California
Nicholas H. Putnam: Independent Researcher
Ivo Gut: Barcelona Institute of Science and Technology
Jay Ghurye: Dovetail Genomics
Erik Garrison: University of California
Ying Sims: Wellcome Sanger Institute
Joanna Collins: Wellcome Sanger Institute
Sarah Pelan: Wellcome Sanger Institute
James Torrance: Wellcome Sanger Institute
Alan Tracey: Wellcome Sanger Institute
Jonathan Wood: Wellcome Sanger Institute
Robel E. Dagnew: University of Southern California
Dengfeng Guan: University of Cambridge
Sarah E. London: University of Chicago
David F. Clayton: Clemson University
Claudio V. Mello: Oregon Health and Science University
Samantha R. Friedrich: Oregon Health and Science University
Peter V. Lovell: Oregon Health and Science University
Ekaterina Osipova: Max Planck Institute of Molecular Cell Biology and Genetics
Farooq O. Al-Ajli: Monash University Malaysia Genomics Facility, School of Science
Simona Secomandi: University of Milan
Heebal Kim: Seoul National University
Constantina Theofanopoulou: The Rockefeller University
Michael Hiller: LOEWE Centre for Translational Biodiversity Genomics
Yang Zhou: BGI-Shenzhen
Robert S. Harris: Pennsylvania State University
Kateryna D. Makova: Pennsylvania State University
Paul Medvedev: Pennsylvania State University
Jinna Hoffman: National Library of Medicine, NIH
Patrick Masterson: National Library of Medicine, NIH
Karen Clark: National Library of Medicine, NIH
Fergal Martin: Wellcome Genome Campus
Kevin Howe: Wellcome Genome Campus
Paul Flicek: Wellcome Genome Campus
Brian P. Walenz: National Human Genome Research Institute, National Institutes of Health
Woori Kwak: eGnome, Inc.
Hiram Clawson: University of California
Mark Diekhans: University of California
Luis Nassar: University of California
Benedict Paten: University of California
Robert H. S. Kraus: University of Konstanz
Andrew J. Crawford: Universidad de los Andes
M. Thomas P. Gilbert: University of Copenhagen
Guojie Zhang: China National Genebank, BGI-Shenzhen
Byrappa Venkatesh: Institute of Molecular and Cell Biology, A*STAR, Biopolis
Robert W. Murphy: Centre for Biodiversity, Royal Ontario Museum
Klaus-Peter Koepfli: Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park
Beth Shapiro: University of California Santa Cruz
Warren E. Johnson: Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park
Federica Palma: University of East Anglia
Tomas Marques-Bonet: Institute of Evolutionary Biology (UPF-CSIC), PRBB
Emma C. Teeling: University College Dublin
Tandy Warnow: The University of Illinois at Urbana-Champaign
Jennifer Marshall Graves: La Trobe University
Oliver A. Ryder: San Diego Zoo Global
David Haussler: University of California
Stephen J. O’Brien: ITMO University
Jonas Korlach: Pacific Biosciences
Harris A. Lewin: University of California Davis
Kerstin Howe: Wellcome Sanger Institute
Eugene W. Myers: Max Planck Institute of Molecular Cell Biology and Genetics
Richard Durbin: University of Cambridge
Adam M. Phillippy: National Human Genome Research Institute, National Institutes of Health
Erich D. Jarvis: The Rockefeller University

Nature, 2021, vol. 592, issue 7856, 737-746

Abstract: Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Date: 2021
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Citations: View citations in EconPapers (14)

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DOI: 10.1038/s41586-021-03451-0

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