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Towards complete and error-free genome assemblies of all vertebrate species
Nature ( IF 50.5 ) Pub Date : 2021-04-28 , DOI: 10.1038/s41586-021-03451-0
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 , Francoise 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 Grutzner ₂₂ , Wesley C Warren ₂₃ , Christopher N Balakrishnan ₂₄ , Dave Burt ₂₅ , Julia M George ₂₆ , Matthew T Biegler ₆ , David Iorns ₂₇ , Andrew 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 William 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 , Sarah B Kingan 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 H Putnam ₅₀ , Ivo 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 , David F Clayton ₅₆ , Claudio V Mello ₅₇ , Samantha R 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 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 J Crawford ₇₅ , M Thomas P Gilbert _{76,

77} , Guojie Zhang _{78,

79,

80,

81} , Byrappa Venkatesh ₈₂ , Robert W Murphy ₈₃ , Klaus-Peter Koepfli ₈₄ , Beth Shapiro _{85,

86} , Warren E Johnson _{84,

87,

88} , Federica Di Palma ₈₉ , Tomas Marques-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 , Eugene W Myers _{15,

40,

102} , Richard Durbin _{2,

3} , Adam M Phillippy ₁ , Erich D Jarvis _{4,

6,

86}

Affiliation

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Department of Genetics, University of Cambridge, Cambridge, UK.
Wellcome Sanger Institute, Cambridge, UK.
Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA.
The Genome Center, University of California Davis, Davis, CA, USA.
Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.
Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany.
Berlin Center for Genomics in Biodiversity Research, Berlin, Germany.
DNAnexus Inc., Mountain View, CA, USA.
Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
University of Southern California, Los Angeles, CA, USA.
National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA.
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
DRESDEN-concept Genome Center, Dresden, Germany.
Novogene, Durham, NC, USA.
Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.
Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
School of Biology, University of St Andrews, St Andrews, UK.
University of Massachusetts Cooperative Fish and Wildlife Research Unit, Amherst, MA, USA.
School of Biological Science, The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia.
Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
Department of Biology, East Carolina University, Greenville, NC, USA.
UQ Genomics, University of Queensland, Brisbane, Queensland, Australia.
Department of Biological Sciences, Clemson University, Clemson, SC, USA.
The Genetic Rescue Foundation, Wellington, New Zealand.
Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand.
Department of Zoology, University of Otago, Dunedin, New Zealand.
University of Arizona Genetics Core, Tucson, AZ, USA.
Department of Life Sciences, Natural History Museum, London, UK.
School of Natural Sciences, Bangor University, Gwynedd, UK.
Department of Biology, University of Konstanz, Konstanz, Germany.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
Department of Biology, University of Antwerp, Antwerp, Belgium.
Naturalis Biodiversity Center, Leiden, The Netherlands.
Institute of Biology, Karl-Franzens University of Graz, Graz, Austria.
Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
Center for Systems Biology, Dresden, Germany.
Zoological Institute, University of Basel, Basel, Switzerland.
Tag.bio, San Francisco, CA, USA.
UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
San Diego Zoo Global, Escondido, CA, USA.
Pacific Biosciences, Menlo Park, CA, USA.
Digital BioLogic, Ivanić-Grad, Croatia.
Bionano Genomics, San Diego, CA, USA.
Arima Genomics, San Diego, CA, USA.
Dovetail Genomics, Santa Cruz, CA, USA.
Independent Researcher, Santa Cruz, CA, USA.
CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
Universitat Pompeu Fabra, Barcelona, Spain.
Department of Computer Science, University of Maryland College Park, College Park, MD, USA.
School of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China.
Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, IL, USA.
Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA.
Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia.
Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia.
Qatar Falcon Genome Project, Doha, Qatar.
Department of Biosciences, University of Milan, Milan, Italy.
eGnome, Inc., Seoul, Republic of Korea.
LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
Senckenberg Research Institute, Frankfurt, Germany.
Goethe-University, Faculty of Biosciences, Frankfurt, Germany.
BGI-Shenzhen, Shenzhen, China.
Department of Biology, Pennsylvania State University, University Park, PA, USA.
Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA.
Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA.
Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA.
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Hoonygen, Seoul, Korea.
Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.
Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
University Museum, NTNU, Trondheim, Norway.
China National Genebank, BGI-Shenzhen, Shenzhen, China.
Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore.
Centre for Biodiversity, Royal Ontario Museum, Toronto, Ontario, Canada.
Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA.
Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, USA.
The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA.
Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Department of Biological Sciences, Earlham Institute, University of East Anglia, Norwich, UK.
Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.
Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.
School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL, USA.
School of Life Science, La Trobe University, Melbourne, Victoria, Australia.
Department of Evolution, Behavior, and Ecology, University of California San Diego, La Jolla, CA, USA.
Laboratory of Genomics Diversity-Center for Computer Technologies, ITMO University, St. Petersburg, Russian Federation.
Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA.
Department of Evolution and Ecology, University of California Davis, Davis, CA, USA.
John Muir Institute for the Environment, University of California Davis, Davis, CA, USA.
Faculty of Computer Science, Technical University Dresden, Dresden, Germany.

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 species^1,2,3,4. To address this issue, the international Genome 10K (G10K) consortium^5,6 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.

中文翻译：

实现所有脊椎动物的完整且无错误的基因组组装

高质量和完整的参考基因组组装是将基因组学应用于生物学、疾病和生物多样性保护的基础。然而，此类组件仅适用于少数非微生物物种^1,2,3,4 。为了解决这个问题，国际 Genome 10K (G10K) 联盟^5,6经过五年的努力，评估和开发了具有成本效益的方法来组装高度准确和近乎完整的参考基因组。在这里，我们介绍了从代表 6 个主要脊椎动物谱系的 16 个物种生成组件中获得的经验教训。我们确认，长读长测序技术对于最大化基因组质量至关重要，并且如果处理不当，未解决的复杂重复和单倍型杂合性是组装错误的主要来源。我们的组装纠正了重大错误，在一些最好的历史参考基因组中添加了缺失的序列，并揭示了生物学发现。其中包括鉴定许多错误的基因重复、基因大小的增加、谱系特有的染色体重排、蝙蝠基因组中重复的独立染色体断点，以及蛋白质编码基因及其调控区域中典型的富含GC的模式。吸取这些经验教训，我们启动了脊椎动物基因组计划 (VGP)，这是一项国际努力，旨在为所有大约 70,000 种现存脊椎动物生成高质量、完整的参考基因组，并帮助开启生命发现的新时代科学。

更新日期：2021-04-28

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