Nature

, volume 592 , issue 7856 , pages 737-746

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

Arang Rhie ¹

Shane A Mccarthy ^{2, 3}

Olivier Fedrigo ⁴

Joana Damas ⁵

Giulio Formenti ^{4, 6}

Sergey Koren ¹

Marcela Uliano-Silva ^{7, 8}

William Chow ³

Arkarachai Fungtammasan ⁹

Juwan Kim ¹⁰

CHUL LEE ¹⁰

Byung June Ko ¹¹

Mark Chaisson ¹²

Gregory L Gedman ⁶

Lindsey J Cantin ⁶

Françoise Thibaud-Nissen ¹³

Leanne Haggerty ¹⁴

Iliana Bista ^{2, 3}

Michelle Smith ³

Bettina Haase ⁴

Jacquelyn Mountcastle ⁴

Sylke Winkler ^{15, 16}

Sadye Paez ^{4, 6}

Jason Howard ¹⁷

Sonja C. Vernes ^{18, 19, 20}

Tanya M Lama ²¹

Frank Grützner ²²

Wesley C. Warren ²³

Christopher N. Balakrishnan ²⁴

David R. Burt ²⁵

John George ²⁶

Matthew T Biegler ⁶

David Iorns ²⁷

Andrew P. Digby ²⁸

Daryl Eason ²⁸

Bruce Robertson ²⁹

Taylor Edwards ³⁰

Mark Wilkinson ³¹

George Turner ³²

Axel Meyer ³³

Andreas F. Kautt ^{33, 34}

Paolo Franchini ³³

H. W. DETRICH ³⁵

Hannes Svardal ^{36, 37}

Maximilian Wagner ³⁸

Gavin J.P. Naylor ³⁹

Martin Pippel ^{15, 40}

Milan Malinsky ^{3, 41}

Mark Mooney ⁴²

Maria Simbirsky ⁹

Brett T Hannigan ⁹

Trevor Pesout ⁴³

Marlys Houck ⁴⁴

Ann Misuraca ⁴⁴

David M. Rank ⁴⁵

Richard Hall ⁴⁵

Zev Kronenberg ⁴⁵

Ivan Sović ^{45, 46}

Christopher Dunn ⁴⁵

Zemin Ning ³

Alex Hastie ⁴⁷

Joyce Lee ⁴⁷

Siddarth Selvaraj ⁴⁸

Richard E. Green ^{43, 49}

NICHOLAS PUTNAM ⁵⁰

Ivo Glynne Gut ^{51, 52}

Jay Ghurye ^{49, 53}

Erik Garrison ⁴³

Ying Sims ³

Joanna Collins ³

Sarah Pelan ³

James Torrance ³

Alan Tracey ³

Jonathan Wood ³

Robel E Dagnew ¹²

Dengfeng Guan ^{2, 54}

Sarah E. London ⁵⁵

D. F. Clayton ⁵⁶

Claudio V. Mello ⁵⁷

Samantha Friedrich ⁵⁷

Peter V Lovell ⁵⁷

Ekaterina Osipova ^{15, 40, 58}

Farooq O Al Ajli ^{59, 60, 61}

Simona Secomandi ⁶²

Heebal Kim ^{10, 11, 63}

Constantina Theofanopoulou ⁶

Michael Hiller ^{64, 65, 66}

Yang Zhou ⁶⁷

ROBERT S. HARRIS ⁶⁸

Kateryna D. Makova ^{68, 69, 70}

Paul Medvedev ^{69, 70, 71, 72}

Jinna Hoffman ¹³

Patrick Masterson ¹³

Karen Clark ¹³

Fergal J Martin ¹⁴

Kevin Howe ¹⁴

Paul Flicek ¹⁴

Brian P. Walenz ¹

Woori Kwak ^{63, 73}

Hiram Clawson ⁴³

Mark Diekhans ⁴³

Luis Nassar ⁴³

Benedict Paten ⁴³

Robert H S Kraus ^{33, 74}

Andrew Crawford ⁷⁵

M. Gilbert ^{76, 77}

Guojie Zhang ^{78, 79, 80, 81}

B. Venkatesh ⁸²

Robert W. Murphy ⁸³

Klaus-Peter Koepfli ⁸⁴

Beth Shapiro ^{85, 86}

Warren D. Johnson ^{84, 87, 88}

Federica Di Palma ⁸⁹

Tomàs Marquès-Bonet ^{90, 91, 92, 93}

Emma C. Teeling ⁹⁴

Tandy Warnow ⁹⁵

Jennifer Marshall Graves ⁹⁶

Oliver A. Ryder ^{44, 97}

David Haussler ^{43, 85}

Stephen J. O'Brien ^{98, 99}

Jonas Korlach ⁴⁵

HARRIS A. LEWIN ^{5, 100, 101}

Kerstin Howe ³

E. W. Myers ^{15, 40, 102}

Richard L. Durbin ^{2, 3}

Adam M. Phillippy ¹

Erich D. Jarvis ^{4, 6, 86}

Hide authors affiliations Show authors affiliations: 102 affiliations

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA |

Department of Genetics, University of Cambridge, Cambridge, UK |

Wellcome Sanger Institute, Cambridge, UK |

⁴

Vertebrate Genome Lab, The Rockefeller University, New York, USA |

⁵

The Genome Center, University of California Davis, Davis, USA |

⁶

Laboratory of Neurogenetics of Language, The Rockefeller University, New York, USA |

⁷

Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany |

⁸

Berlin Center for Genomics in Biodiversity Research, Berlin, Germany |

⁹

DNAnexus Inc., Mountain View, USA |

¹⁰

Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea |

¹¹

Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea |

¹²

University of Southern California, Los angeles, USA |

¹³

National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA

United States National Library of Medicine

National Center for Biotechnology Information

¹⁴

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK |

¹⁵

Max Planck institute of Molecular Cell Biology and Genetics, Dresden, Germany |

¹⁶

DRESDEN-concept Genome Center, Dresden, Germany |

¹⁷

Novogene, Durham, USA |

¹⁸

Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands |

¹⁹

Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands |

²⁰

School of Biology, University of St Andrews, St Andrews, UK |

²¹

University of Massachusetts Cooperative Fish and Wildlife Research Unit, Amherst, USA |

²²

School of Biological Science, The Environment Institute, University of Adelaide, Adelaide, Australia |

²³

Bond Life Sciences Center, University of Missouri, Columbia, USA |

²⁴

Department of Biology, East Carolina University, Greenville, USA |

²⁵

UQ Genomics, University of Queensland, Brisbane, Australia |

²⁶

Department of Biological Sciences, Clemson University, Clemson, USA |

²⁷

The Genetic Rescue Foundation, Wellington, New Zealand |

²⁸

Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand |

²⁹

Department of Zoology, University of Otago, Dunedin, New Zealand |

³⁰

University of Arizona Genetics Core, Tucson, USA |

³¹

Department of life sciences, Natural History Museum, London, UK |

³²

School of Natural Sciences, Bangor University, Gwynedd, UK |

³³

Department of Biology, University of Konstanz, Konstanz, Germany |

³⁴

Department of Organismic and Evolutionary Biology, Harvard university, Cambridge, USA |

³⁵

Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, USA |

³⁶

Department of Biology, University of Antwerp, Antwerp, Belgium |

³⁷

Naturalis Biodiversity Center, Leiden, the Netherlands |

³⁸

Institute of Biology, Karl-Franzens University of Graz, Graz, Austria |

³⁹

Florida Museum of Natural History, University of Florida, Gainesville, USA |

⁴⁰

Center for Systems Biology, Dresden, Germany |

⁴¹

Zoological Institute, University of Basel, Basel, Switzerland |

⁴²

Tag.bio, San Francisco, USA |

⁴³

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA |

⁴⁴

San Diego Zoo Global, Escondido, USA |

⁴⁵

Pacific Biosciences, Menlo Park, USA |

⁴⁶

Digital BioLogic, Ivanić-Grad, Croatia |

⁴⁷

BioNano Genomics, San Diego, USA |

⁴⁸

Arima Genomics, San Diego, USA |

⁴⁹

Dovetail Genomics, Santa Cruz, USA |

⁵⁰

Independent Researcher, Santa Cruz, USA |

⁵¹

CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain

Barcelona Institute for Science and Technology

Centre for Genomic Regulation

⁵²

Universitat Pompeu Fabra, Barcelona, Spain |

⁵³

Department of Computer Science, University of Maryland College Park, College Park, USA |

⁵⁴

School of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China |

⁵⁵

Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, USA |

⁵⁶

Department of Genetics and Biochemistry, Clemson University, Clemson, USA |

⁵⁷

Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, USA |

⁵⁸

Max Planck Institute For The Physics Of Complex Systems, Dresden, Germany |

⁵⁹

Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia |

⁶⁰

Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia |

⁶¹

Qatar Falcon Genome Project, Doha, Qatar |

⁶²

Department of BioSciences, University of Milan, Milan, Italy |

⁶³

eGnome, Inc., Seoul, Republic of Korea |

⁶⁴

LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany |

⁶⁵

Senckenberg Research Institute, Frankfurt, Germany |

⁶⁶

Goethe-University, Faculty of Biosciences, Frankfurt, Germany |

⁶⁷

BGI-shenzhen, Shenzhen, China |

⁶⁸

Department of Biology, Pennsylvania State University, University Park, USA |

⁶⁹

Center for Medical Genomics, Pennsylvania State University, University Park, USA |

⁷⁰

Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, USA |

⁷¹

Department of Computer Science and Engineering, Pennsylvania State University, University Park, USA |

⁷²

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, USA |

⁷³

Hoonygen, Seoul, Korea |

⁷⁴

Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany |

⁷⁵

Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia |

⁷⁶

Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark |

⁷⁷

University Museum, NTNU, Trondheim, Norway |

⁷⁸

China National GeneBank, BGI-Shenzhen, Shenzhen, China |

⁷⁹

Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark |

⁸⁰

State Key laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China |

⁸¹

Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China |

⁸²

Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore |

⁸³

Centre for Biodiversity, Royal Ontario Museum, Toronto, Canada |

⁸⁴

Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, USA |

⁸⁵

Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, USA |

⁸⁶

Howard Hughes Medical Institute, Chevy Chase, USA |

⁸⁷

The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, USA |

⁸⁸

Walter Reed Army Institute of Research, Silver Spring, USA |

⁸⁹

Department of Biological Sciences, Earlham Institute, University of East Anglia, Norwich, UK |

⁹⁰

Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain

Barcelona Biomedical Research Park

Institut de Biologia Evolutiva

⁹¹

Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain |

⁹²

Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

Barcelona Institute for Science and Technology

Centre for Genomic Regulation

⁹³

Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain

Autonomous University of Barcelona

Catalan Institute of Palaeontology Miquel Crusafont

⁹⁴

School of Biology and Environmental Science, University College Dublin, Dublin, Ireland |

⁹⁵

Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, USA |

⁹⁶

School of Life Science, La Trobe University, Melbourne, Australia |

⁹⁷

Department of Evolution, Behavior, and Ecology, University of California San Diego, La Jolla, USA |

⁹⁸

Laboratory of Genomics Diversity-Center for Computer Technologies, ITMO University, St. Petersburg, Russian Federation |

⁹⁹

Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, USA |

¹⁰⁰

Department of Evolution and Ecology, University of California Davis, Davis, USA |

¹⁰¹

John Muir Institute for the Environment, University of California Davis, Davis, USA |

¹⁰²

Faculty of Computer Science, Technical University Dresden, Dresden, Germany |

Publication type: Journal Article

Publication date: 2021-04-28

Springer Nature

Nature

scimago Q1

wos Q1

SJR: 18.288

CiteScore: 78.1

Impact factor: 48.5

ISSN: 00280836, 14764687

DOI: 10.1038/s41586-021-03451-0

Copy DOI

PubMed ID: 33911273

Multidisciplinary

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. The Vertebrate Genome Project has used an optimized pipeline to generate high-quality genome assemblies for sixteen species (representing all major vertebrate classes), which have led to new biological insights.

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Rhie A. et al. Towards complete and error-free genome assemblies of all vertebrate species // Nature. 2021. Vol. 592. No. 7856. pp. 737-746.

GOST all authors (up to 50) Copy

Rhie A. et al. Towards complete and error-free genome assemblies of all vertebrate species // Nature. 2021. Vol. 592. No. 7856. pp. 737-746.

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BibTex (up to 50 authors) Copy

@article{2021_Rhie,

author = {Arang Rhie and Shane A Mccarthy and Olivier Fedrigo and Joana Damas and Giulio Formenti and Sergey Koren and Marcela Uliano-Silva and William Chow and Arkarachai Fungtammasan and Juwan Kim and CHUL LEE and Byung June Ko and Mark Chaisson and Gregory L Gedman and Lindsey J Cantin and Françoise Thibaud-Nissen and Leanne Haggerty and Iliana Bista and Michelle Smith and Bettina Haase and Jacquelyn Mountcastle and Sylke Winkler and Sadye Paez and Jason Howard and Sonja C. Vernes and Tanya M Lama and Frank Grützner and Wesley C. Warren and Christopher N. Balakrishnan and David R. Burt and John George and Matthew T Biegler and David Iorns and Andrew P. Digby and Daryl Eason and Bruce Robertson and Taylor Edwards and Mark Wilkinson and George Turner and Axel Meyer and Andreas F. Kautt and Paolo Franchini and H. W. DETRICH and Hannes Svardal and Maximilian Wagner and Gavin J.P. Naylor and Martin Pippel and Milan Malinsky and Mark Mooney and Maria Simbirsky and others},

title = {Towards complete and error-free genome assemblies of all vertebrate species},

journal = {Nature},

year = {2021},

volume = {592},

publisher = {Springer Nature},

month = {apr},

url = {https://doi.org/10.1038/s41586-021-03451-0},

number = {7856},

pages = {737--746},

doi = {10.1038/s41586-021-03451-0}

}

MLA

Cite this

MLA Copy

Rhie, Arang, et al. “Towards complete and error-free genome assemblies of all vertebrate species.” Nature, vol. 592, no. 7856, Apr. 2021, pp. 737-746. https://doi.org/10.1038/s41586-021-03451-0.

Publisher

Springer Nature

Journal

Nature

scimago Q1

wos Q1

SJR

18.288

CiteScore

78.1

Impact factor

48.5

ISSN

00280836 (Print)

14764687 (Electronic)

Profiles

Olivier Fedrigo