Recovering individual haplotypes and a contiguous genome assembly from pooled long-read sequencing of the diamondback moth (Lepidoptera: Plutellidae).
Recovering individual haplotypes and a contiguous genome assembly from pooled long-read sequencing of the diamondback moth (Lepidoptera: Plutellidae).
复制标题
DOI：
10.1093/g3journal/jkac210
复制
发表时间：
2022-09-30
期刊：
影响因子：
--
通讯作者：
中科院分区：
文献类型：
--
作者：
由于这些数据中技术测序错误、基因座内遗传变异和基因座间相似性的重叠分布，使用嘈杂的长读段数据组装不同的单倍型对单倍体基因组组装的重建提出了挑战。在这里，我们提出了一个比较分析的组装算法，代表布局共识，重复图，和de Bruijn图的方法。我们研究如何后处理策略，试图减少冗余杂合性与初始组装算法的选择相互作用，并最终产生一系列的染色体水平的农业害虫，小菜蛾，小菜蛾（L.）的组件。我们比较了评价方法，并表明BUSCO分析可能高估了单倍体去除处理在长读草案基因组，在比较的k-聚体方法。我们讨论了权衡固有的组装算法和策展的选择，并建议“最佳实践”是研究问题的依赖。我们证明了等位基因分歧和等位基因衍生的重叠群冗余最终基因组组装之间的联系，并记录冗余序列之间的编码和非编码多样性的模式。我们还记录了过量的非同义多态性和单倍体组装或后组装算法未解决之间的联系。最后，我们讨论了这种现象如何可能有相关的使用嘈杂的长读基因组组装在比较基因组学。
The assembly of divergent haplotypes using noisy long-read data presents a challenge to the reconstruction of haploid genome assemblies, due to overlapping distributions of technical sequencing error, intralocus genetic variation, and interlocus similarity within these data. Here, we present a comparative analysis of assembly algorithms representing overlap-layout-consensus, repeat graph, and de Bruijn graph methods. We examine how postprocessing strategies attempting to reduce redundant heterozygosity interact with the choice of initial assembly algorithm and ultimately produce a series of chromosome-level assemblies for an agricultural pest, the diamondback moth, Plutella xylostella (L.). We compare evaluation methods and show that BUSCO analyses may overestimate haplotig removal processing in long-read draft genomes, in comparison to a k-mer method. We discuss the trade-offs inherent in assembly algorithm and curation choices and suggest that “best practice” is research question dependent. We demonstrate a link between allelic divergence and allele-derived contig redundancy in final genome assemblies and document the patterns of coding and noncoding diversity between redundant sequences. We also document a link between an excess of nonsynonymous polymorphism and haplotigs that are unresolved by assembly or postassembly algorithms. Finally, we discuss how this phenomenon may have relevance for the usage of noisy long-read genome assemblies in comparative genomics.
登录
查看更多内容
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
3.7
作者：
Baxter SW;Davey JW;Johnston JS;Shelton AM;Heckel DG;Jiggins CD;Blaxter ML
通讯作者：
Blaxter ML
影响因子：
64.8
作者：
Armstrong J;Hickey G;Diekhans M;Fiddes IT;Novak AM;Deran A;Fang Q;Xie D;Feng S;Stiller J;Genereux D;Johnson J;Marinescu VD;Alföldi J;Harris RS;Lindblad-Toh K;Haussler D;Karlsson E;Jarvis ED;Zhang G;Paten B
通讯作者：
Paten B
影响因子：
48
作者：
Cheng H;Concepcion GT;Feng X;Zhang H;Li H
通讯作者：
Li H