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

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)...

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Detalhes bibliográficos
Autores: Rhie, Arang|||0000-0002-9809-8127, McCarthy, Shane A., Fedrigo, Olivier|||0000-0002-6450-7551, Damas, Joana, Formenti, Giulio|||0000-0002-7554-5991, Koren, Sergey|||0000-0002-1472-8962, Uliano da Silva, Marcela|||0000-0001-6723-4715, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul|||0000-0002-9403-0774, Ko, Byung June|||0000-0002-5683-7438, Chaisson, Mark|||0000-0001-5395-1457, Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Françoise|||0000-0003-4957-7807, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina|||0000-0001-8945-7282, Mountcastle, Jacquelyn|||0000-0003-1078-4905, Winkler, Sylke|||0000-0002-0915-3316, Paez, Sadye, Howard, Jason, Vernes, Sonja C.|||0000-0003-0305-4584, Lama, Tanya M., Marquès i Bonet, Tomàs|||0000-0002-5597-3075, Warren, Wesley|||0000-0003-2255-2730, Balakrishnan, Christopher N., Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Pippel, Martin|||0000-0002-8134-5929, Malinsky, Milan|||0000-0002-1462-6317, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B., Hall, Richard|||0000-0001-6490-8227, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher|||0000-0001-7896-1512, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E.|||0000-0003-0516-5827, Putnam, Nicholas H., Gut, Ivo|||0000-0001-7219-632X, Ghurye, Jay, Garrison, Erik|||0000-0003-3821-631X, Sims, Ying|||0000-0003-4765-4872, Collins, Joanna|||0000-0001-5782-5028, Pelan, Sarah, Torrance, James, Tracey, Alan|||0000-0002-4805-9058, Wood, Jonathan|||0000-0002-7545-2162, Dagnew, Robel E., Guan, Dengfeng|||0000-0002-6376-3940, London, Sarah E., Clayton, David F., Mello, Claudio V.|||0000-0002-9826-8421, Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina|||0000-0002-6769-7223, Al-Ajli, Farooq O., Secomandi, Simona|||0000-0001-8597-6034, Kim, Heebal|||0000-0003-3064-1303, Theofanopoulou, Constantina|||0000-0003-2014-7563, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal J.|||0000-0002-1672-050X, Howe, Kevin, Flicek, Paul|||0000-0002-3897-7955, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Diekhans, Mark|||0000-0002-0430-0989, Nassar, Luis, Paten, Benedict|||0000-0001-8863-3539, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P.|||0000-0002-5805-7195, Zhang, Guojie|||0000-0001-6860-1521, Venkatesh, Byrappa, Murphy, Robert W.|||0000-0001-8555-2338, Koepfli, Klaus-Peter|||0000-0001-7281-0676, Shapiro, Beth|||0000-0002-2733-7776, Johnson, Warren E.|||0000-0002-5954-186X, Di Palma, Federica, Teeling, Emma C., Warnow, Tandy, Marshall Graves, Jennifer A.|||0000-0001-6480-7856, Ryder, Oliver A.|||0000-0003-2427-763X, Haussler, David, O'Brien, Stephen J.|||0000-0001-7353-8301, Korlach, Jonas|||0000-0003-3047-4250, Lewin, Harris A.|||0000-0002-1043-7287, Howe, Kerstin|||0000-0003-2237-513X, Myers, Eugene W.|||0000-0002-6580-7839, Durbin, Richard|||0000-0002-9130-1006, Phillippy, Adam M.|||0000-0003-2983-8934, Jarvis, Erich|||0000-0001-8931-5049
Formato: artículo
Fecha de publicación:2021
País:España
Recursos:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:239763
Acesso em linha:https://ddd.uab.cat/record/239763
https://dx.doi.org/urn:doi:10.1038/s41586-021-03451-0
Access Level:acceso abierto
Palavra-chave:Evolutionary genetics
Genome assembly algorithms
Molecular evolution
Research data
Descrição
Resumo: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.

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