Towards complete and error-free genome assemblies of all vertebrate species
Rhie, Arang (National Institutes of Health. National Human Genome Research Institute (USA))
McCarthy, Shane A. (University of Cambridge. Department of Genetics (UK))
Fedrigo, Olivier (The Rockefeller University. Vertebrate Genome Lab (USA))
Damas, Joana (University of California Davis. The Genome Center (USA))
Formenti, Giulio (The Rockefeller University. Vertebrate Genome Lab (USA))
Koren, Sergey (National Institutes of Health. National Human Genome Research Institute (USA))
Uliano da Silva, Marcela (Leibniz Institute for Zoo and Wildlife Research. Department of Evolutionary Genetics (Germany))
Chow, William (Wellcome Trust Sanger Institute (Regne Unit))
Fungtammasan, Arkarachai (DNAnexus Inc. (USA))
Kim, Juwan (Seoul National University. Interdisciplinary Program in Bioinformatics (Republic of Korea))
Lee, Chul (Seoul National University. Interdisciplinary Program in Bioinformatics (Republic of Korea))
Ko, Byung June (Seoul National University. Department of Agricultural Biotechnology (Republic of Korea))
Chaisson, Mark (University of Southern California (USA))
Gedman, Gregory L. (The Rockefeller University. Laboratory of Neurogenetics of Language (USA))
Cantin, Lindsey J. (The Rockefeller University. Laboratory of Neurogenetics of Language (USA))
Thibaud-Nissen, Françoise (National Library of Medicine. National Center for Biotechnology Information (USA))
Haggerty, Leanne (European Bioinformatics Institute. European Molecular Biology Laboratory (UK))
Bista, Iliana (University of Cambridge. Department of Genetics (UK))
Smith, Michelle (Wellcome Trust Sanger Institute (Regne Unit))
Haase, Bettina (The Rockefeller University. Vertebrate Genome Lab (USA))
Mountcastle, Jacquelyn (The Rockefeller University. Vertebrate Genome Lab (USA))
Winkler, Sylke (Max Planck Institute of Molecular Cell Biology and Genetics (Germany))
Paez, Sadye (The Rockefeller University. Vertebrate Genome Lab (USA))
Howard, Jason (Novogene (USA))
Vernes, Sonja C. (Donders Institute for Brain, Cognition and Behaviour (The Netherlands))
Lama, Tanya M. (University of Massachusetts. Cooperative Fish and Wildlife Research Unit (USA))
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Warren, Wesley (University of Missouri. Bond Life Sciences Center (USA))
Balakrishnan, Christopher N. (East Carolina University. Department of Biology (USA))
Burt, Dave (University of Queensland. UQ Genomics (Australia))
George, Julia M. (Clemson University. Department of Biological Sciences (USA))
Biegler, Matthew T. (The Rockefeller University. Laboratory of Neurogenetics of Language (USA))
Iorns, David (The Genetic Rescue Foundation (New Zealand))
Digby, Andrew (Kākāpō Recovery, Department of Conservation (New Zealand))
Eason, Daryl (Kākāpō Recovery, Department of Conservation (New Zealand))
Robertson, Bruce (University of Otago. Department of Zoology (New Zealand))
Edwards, Taylor (University of Arizona Genetics Core (USA))
Wilkinson, Mark (Natural History Museum. Department of Life Sciences (UK))
Turner, George (Bangor University. School of Natural Sciences (UK))
Meyer, Axel (University of Konstanz. Department of Biology (Germany))
Kautt, Andreas F. (University of Konstanz. Department of Biology (Germany))
Franchini, Paolo (University of Konstanz. Department of Biology (Germany))
Detrich III, H. William (Northeastern University Marine Science Center. Department of Marine and Environmental Sciences (USA))
Svardal, Hannes (University of Antwerp. Department of Biology (Belgium))
Wagner, Maximilian (Karl-Franzens University of Graz. Institute of Biology (Austria))
Naylor, Gavin J. P. (University of Florida. Florida Museum of Natural History (USA))
Pippel, Martin (Max Planck Institute of Molecular Cell Biology and Genetics (Germany))
Malinsky, Milan (University of Basel. Zoological Institute (Switzerland))
Mooney, Mark (Tag.bio (USA))
Simbirsky, Maria (DNAnexus Inc. (USA))
Hannigan, Brett T. (DNAnexus Inc. (USA))
Pesout, Trevor (University of California. UC Santa Cruz Genomics Institute (USA))
Houck, Marlys (San Diego Zoo Global (USA))
Misuraca, Ann (San Diego Zoo Global (USA))
Kingan, Sarah B. (Pacific Biosciences (USA))
Hall, Richard (Pacific Biosciences (USA))
Kronenberg, Zev (Pacific Biosciences (USA))
Sović, Ivan (Pacific Biosciences (USA))
Dunn, Christopher (Pacific Biosciences (USA))
Ning, Zemin (Wellcome Trust Sanger Institute (Regne Unit))
Hastie, Alex (Bionano Genomics (USA))
Lee, Joyce (Bionano Genomics (USA))
Selvaraj, Siddarth (Arima Genomics (USA))
Green, Richard E. (University of California. UC Santa Cruz Genomics Institute (USA))
Putnam, Nicholas H. (Independent Researcher. Santa Cruz (USA))
Gut, Ivo (Centro Nacional de Análisis Genómico. Instituto de Ciencia y Tecnología de Barcelona)
Ghurye, Jay (University of Maryland College Park. Department of Computer Science (USA))
Garrison, Erik (University of California. UC Santa Cruz Genomics Institute (USA))
Sims, Ying (Wellcome Trust Sanger Institute (Regne Unit))
Collins, Joanna (Wellcome Trust Sanger Institute (Regne Unit))
Pelan, Sarah (Wellcome Trust Sanger Institute (Regne Unit))
Torrance, James (Wellcome Trust Sanger Institute (Regne Unit))
Tracey, Alan (Wellcome Trust Sanger Institute (Regne Unit))
Wood, Jonathan (Wellcome Trust Sanger Institute (Regne Unit))
Dagnew, Robel E. (University of Southern California (USA))
Guan, Dengfeng (Harbin Institute of Technology. Center for Bioinformatics. School of Computer Science and Technology (China))
London, Sarah E. (University of Chicago. Institute for Mind and Biology. Department of Psychology (USA))
Clayton, David F. (Clemson University. Department of Genetics and Biochemistry (USA))
Mello, Claudio V. (Oregon Health and Science University. Department of Behavioral Neuroscience (USA))
Friedrich, Samantha R. (Oregon Health and Science University. Department of Behavioral Neuroscience (USA))
Lovell, Peter V. (Oregon Health and Science University. Department of Behavioral Neuroscience (USA))
Osipova, Ekaterina (Max Planck Institute for the Physics of Complex Systems (Germany))
Al-Ajli, Farooq O. (Monash University Malaysia. Tropical Medicine and Biology Multidisciplinary Platform (Malaysia))
Secomandi, Simona (University of Milan. Department of Biosciences (Italy))
Kim, Heebal (Seoul National University. Interdisciplinary Program in Bioinformatics (Republic of Korea))
Theofanopoulou, Constantina (The Rockefeller University. Laboratory of Neurogenetics of Language (USA))
Hiller, Michael (Goethe-University. Faculty of Biosciences (Germany))
Zhou, Yang (BGI-Shenzhen (China))
Harris, Robert S. (Pennsylvania State University. Department of Biology (USA))
Makova, Kateryna D. (Pennsylvania State University. Department of Biology (USA))
Medvedev, Paul (Pennsylvania State University. Center for Medical Genomics (USA))
Hoffman, Jinna (National Library of Medicine. National Center for Biotechnology Information (USA))
Masterson, Patrick (National Library of Medicine. National Center for Biotechnology Information (USA))
Clark, Karen (National Library of Medicine. National Center for Biotechnology Information (USA))
Martin, Fergal J. (European Bioinformatics Institute. European Molecular Biology Laboratory (UK))
Howe, Kevin (European Bioinformatics Institute. European Molecular Biology Laboratory (UK))
Flicek, Paul (European Bioinformatics Institute. European Molecular Biology Laboratory (UK))
Walenz, Brian P. (National Institutes of Health. National Human Genome Research Institute (USA))
Kwak, Woori (eGnome, Inc. (Republic of Korea))
Clawson, Hiram (University of California. UC Santa Cruz Genomics Institute (USA))
Diekhans, Mark (University of California. UC Santa Cruz Genomics Institute (USA))
Nassar, Luis (University of California. UC Santa Cruz Genomics Institute (USA))
Paten, Benedict (University of California. UC Santa Cruz Genomics Institute (USA))
Kraus, Robert H. S. (Max Planck Institute of Animal Behavior. Department of Migration (Germany))
Crawford, Andrew J. (Universidad de los Andes. Department of Biological Sciences (Colombia))
Gilbert, M. Thomas P. (University of Copenhagen. The GLOBE Institute. Center for Evolutionary Hologenomics (Denmark))
Zhang, Guojie (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics (China))
Venkatesh, Byrappa (A*STAR. Institute of Molecular and Cell Biology (Singapore))
Murphy, Robert W. (Royal Ontario Museum. Centre for Biodiversity (Canada))
Koepfli, Klaus-Peter (Smithsonian Conservation Biology Institute)
Shapiro, Beth (Howard Hughes Medical Institute (USA))
Johnson, Warren E. (Smithsonian Conservation Biology Institute)
Di Palma, Federica (University of East Anglia. Earlham Institute. Department of Biological Sciences (UK))
Teeling, Emma C. (University College Dublin. School of Biology and Environmental Science (Ireland))
Warnow, Tandy (The University of Illinois at Urbana-Champaign. Department of Computer Science (USA))
Graves, Jennifer Marshall (La Trobe University. School of Life Science (Australia))
Ryder, Oliver A. (University of California San Diego. Department of Evolution, Behavior, and Ecology (USA))
Haussler, David (University of California Santa Cruz. Department of Ecology and Evolutionary Biology (USA))
O'Brien, Stephen J. (ITMO University. Laboratory of Genomics Diversity-Center for Computer Technologies (Russian Federation))
Korlach, Jonas (Pacific Biosciences (USA))
Lewin, Harris A. (University of California Davis. John Muir Institute for the Environment (USA))
Howe, Kerstin (Wellcome Trust Sanger Institute (Regne Unit))
Myers, Eugene W. (Max Planck Institute of Molecular Cell Biology and Genetics (Germany))
Durbin, Richard (University of Cambridge. Department of Genetics (UK))
Phillippy, Adam M. (National Institutes of Health. National Human Genome Research Institute (USA))
Jarvis, Erich (The Rockefeller University. Vertebrate Genome Lab (USA))

Data:	2021
Resum:	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.
Ajuts:	European Commission. Horizon 2020 750747 European Commission. Horizon 2020 864203 Ministerio de Economía, Industria y Competitividad BFU2017-86471-P Ministerio de Ciencia e Innovación CEX2018-000792-M Agència de Gestió d'Ajuts Universitaris i de Recerca 2017/SGR-880 European Commission 311000 European Commission. Horizon 2020 681396
Nota:	Altres ajuts: Obra Social "La Caixa" and CERCA Programme/Generalitat de Catalunya
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Evolutionary genetics ; Genome assembly algorithms ; Molecular evolution ; Research data
Publicat a:	Nature, Vol. 592 (April 2021) , p. 737-746, ISSN 1476-4687

DOI: 10.1038/s41586-021-03451-0
PMID: 33911273

32 p, 22.5 MB

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