De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads.
De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads.
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DOI：
10.1093/gigascience/gix085
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发表时间：
2017-10-01
期刊：
影响因子：
9.2
通讯作者：
Jarvis ED
中科院分区：
文献类型：
--
作者：
Korlach J;Gedman G;Kingan SB;Chin CS;Howard JT;Audet JN;Cantin L;Jarvis ED
高质量的基因组有望为研究基因结构、功能和进化提供资源。然而，通常情况下，感兴趣的基因没有完全或准确地组装起来，导致在分析中出现未知的错误或为正确的序列进行额外的克隆工作。一个有希望的解决方案是长时间阅读测序。在这里，我们测试了基于PacBio的长读测序和二倍体组装，以寻找对基于桑格的中读斑雀参考和基于Illumina的短读安娜的蜂鸟参考的潜在改进，这两个发声学习鸟类在神经科学和基因组学中被广泛研究。用相同个体的DNA来产生参考基因组，我们用猎鹰-解压装配器产生了二倍体组装，产生了在百万碱基范围内没有间隙的重叠群，分别比目前的斑马雀和蜂鸟的参考序列提高了150倍和200倍。这些长阅读和分阶段的组装纠正和解决了我们在参考文献中发现的大量错误组装，包括缺口中的缺失序列、缺口两侧的错误序列、难以测序区域的碱基呼叫错误、复杂的重复结构错误以及两个单倍型之间的等位基因差异。这些改进通过单一的长基因组和转录组读取得到了验证，并首次产生了完全分解的蛋白质编码基因，这些基因在神经科学中被广泛研究，并专门用于发声学习物种。这些发现证明了长阅读、以前难以测序的区域的测序以及单倍型的阶段化对产生理解基因结构、功能和进化所需的高质量组装的影响。
Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna's hummingbird reference, 2 vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range, representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read and phased assemblies corrected and resolved what we discovered to be numerous misassemblies in the references, including missing sequences in gaps, erroneous sequences flanking gaps, base call errors in difficult-to-sequence regions, complex repeat structure errors, and allelic differences between the 2 haplotypes. These improvements were validated by single long-genome and transcriptome reads and resulted for the first time in completely resolved protein-coding genes widely studied in neuroscience and specialized in vocal learning species. These findings demonstrate the impact of long reads, sequencing of previously difficult-to-sequence regions, and phasing of haplotypes on generating the high-quality assemblies necessary for understanding gene structure, function, and evolution.
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影响因子：
2.5
作者：
Jarvis, Erich D.;Yu, Jing;Rivas, Miriam V.;Horita, Haruhito;Feenders, Gesa;Whitney, Osceola;Jarvis, Syrus C.;Jarvis, Electra R.;Kubikova, Lubica;Puck, Ana E. P.;Siang-Bakshi, Connie;Martin, Suzanne;McElroy, Michael;Hara, Erina;Howard, Jason;Pfenning, Andreas;Mouritsen, Henrik;Chen, Chun-Chun;Wada, Kazuhiro
通讯作者：
Wada, Kazuhiro
大脑通路复制的大脑进化。
DOI：
10.1098/rstb.2015.0056
发表时间：
2015-12-19
期刊：
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
影响因子：
--
作者：
Chakraborty M;Jarvis ED
通讯作者：
Jarvis ED
DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G
DOI：
10.1126/science.aae0344
发表时间：
2016-04-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gordon D;Huddleston J;Chaisson MJ;Hill CM;Kronenberg ZN;Munson KM;Malig M;Raja A;Fiddes I;Hillier LW;Dunn C;Baker C;Armstrong J;Diekhans M;Paten B;Shendure J;Wilson RK;Haussler D;Chin CS;Eichler EE
通讯作者：
Eichler EE
DOI：
10.1126/science.1254449
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Green RE;Braun EL;Armstrong J;Earl D;Nguyen N;Hickey G;Vandewege MW;St John JA;Capella-Gutiérrez S;Castoe TA;Kern C;Fujita MK;Opazo JC;Jurka J;Kojima KK;Caballero J;Hubley RM;Smit AF;Platt RN;Lavoie CA;Ramakodi MP;Finger JW Jr;Suh A;Isberg SR;Miles L;Chong AY;Jaratlerdsiri W;Gongora J;Moran C;Iriarte A;McCormack J;Burgess SC;Edwards SV;Lyons E;Williams C;Breen M;Howard JT;Gresham CR;Peterson DG;Schmitz J;Pollock DD;Haussler D;Triplett EW;Zhang G;Irie N;Jarvis ED;Brochu CA;Schmidt CJ;McCarthy FM;Faircloth BC;Hoffmann FG;Glenn TC;Gabaldón T;Paten B;Ray DA
通讯作者：
Ray DA