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

	Towards complete and error-free genome assemblies of all vertebrate species
	Rhie, A; McCarthy, SA; Fedrigo, O; Damas, J; Formenti, G; Koren, S; Uliano-Silva, M; Chow, W; Fungtammasan, A; Kim, J; Lee, C; Ko, BJ; Chaisson, M; Gedman, GL; Cantin, LJ; Thibaud-Nissen, F; Haggerty, L; Bista, I; Smith, M; Haase, B; Mountcastle, J; Winkler, S; Paez, S; Howard, J; Vernes, SC; Lama, TM; Grutzner, F; Warren, WC; Balakrishnan, CN; Burt, D; George, JM; Biegler, MT; Iorns, D; Digby, A; Eason, D; Robertson, B; Edwards, T; Wilkinson, M; Turner, G; Meyer, A; Kautt, AF; Franchini, P; Detrich, HW; Svardal, H; Wagner, M; Naylor, GJP; Pippel, M; Malinsky, M; Mooney, M; Simbirsky, M; Hannigan, BT; Pesout, T; Houck, M; Misuraca, A; Kingan, SB; Hall, R; Kronenberg, Z; Sovi, I; Dunn, C; Ning, Z; Hastie, A; Lee, J; Selvaraj, S; Green, RE; Putnam, NH; Gut, I; Ghurye, J; Garrison, E; Sims, Y; Collins, J; Pelan, S; Torrance, J; Tracey, A; Wood, J; Dagnew, RE; Guan, D; London, SE; Clayton, DF; Mello, CV; Friedrich, SR; Lovell, PV; Osipova, E; Al-Ajli, FO; Secomandi, S; Kim, H; Theofanopoulou, C; Hiller, M; Zhou, Y; Harris, RS; Makova, KD; Medvedev, P; Hoffman, J; Masterson, P; Clark, K; Martin, F; Howe, K; Flicek, P; Walenz, BP; Kwak, W; Clawson, H; Diekhans, M; Nassar, L; Paten, B; Kraus, RHS; Crawford, AJ; Gilbert, MTP; Zhang, G; Venkatesh, B; Murphy, RW; Koepfli, KP; Shapiro, B; Johnson, WE; Di Palma, F; Marques-Bonet, T; Teeling, EC; Warnow, T; Graves, JM; Ryder, OA; Haussler, D; O'Brien, SJ; Korlach, J; Lewin, HA; Howe, K; Myers, EW; Durbin, R; Phillippy, AM; Jarvis, ED
	2021
发表期刊	NATURE
ISSN	0028-0836
卷号	592 期号:7856 页码:737-+
摘要	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. 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(1-4). 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.
收录类别	sci
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/13461
专题	科研部门_遗传多样性基因组学研究组（张国捷）
推荐引用方式 GB/T 7714	Rhie, A,McCarthy, SA,Fedrigo, O,et al. Towards complete and error-free genome assemblies of all vertebrate species[J]. NATURE,2021,592(7856):737-+.
APA	Rhie, A.,McCarthy, SA.,Fedrigo, O.,Damas, J.,Formenti, G.,...&Jarvis, ED.(2021).Towards complete and error-free genome assemblies of all vertebrate species.NATURE,592(7856),737-+.
MLA	Rhie, A,et al."Towards complete and error-free genome assemblies of all vertebrate species".NATURE 592.7856(2021):737-+.

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2023031570.pdf（23042KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文