Towards complete and error-free genome assemblies of all vertebrate species.
Towards complete and error-free genome assemblies of all vertebrate species.
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DOI：
10.1038/s41586-021-03451-0
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发表时间：
2021-04
期刊：
影响因子：
64.8
通讯作者：
Jarvis ED
中科院分区：
文献类型：
--
作者：
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 3rd;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;Sović 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
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。为了解决这个问题，国际 Genome 10K (G10K) 联盟花了五年的时间来评估和开发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 个现存脊椎动物物种生成高质量、完整的参考基因组，并帮助开启生命科学发现的新时代。脊椎动物基因组计划使用优化的流程为 16 个物种（代表所有主要脊椎动物类别）生成高质量的基因组组件，从而带来了新的生物学见解。
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. To address this issue, the international Genome 10K (G10K) consortium 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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影响因子：
48
作者：
Chin, Chen-Shan;Peluso, Paul;Schatz, Michael C.
通讯作者：
Schatz, Michael C.
影响因子：
7
作者：
Bishara A;Liu Y;Weng Z;Kashef-Haghighi D;Newburger DE;West R;Sidow A;Batzoglou S
通讯作者：
Batzoglou S
影响因子：
3
作者：
Camacho C;Coulouris G;Avagyan V;Ma N;Papadopoulos J;Bealer K;Madden TL
通讯作者：
Madden TL
DOI：
10.1073/pnas.1210366109
发表时间：
2012-07-31
影响因子：
11.1
作者：
Brandl, Katharina;Tomisato, Wataru;Beutler, Bruce
通讯作者：
Beutler, Bruce
影响因子：
48
作者：
Chin, Chen-Shan;Alexander, David H.;Korlach, Jonas
通讯作者：
Korlach, Jonas