Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data.
Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data.
复制标题
利用长阅读和低深度后代数据对四倍体马铃薯基因组进行单倍型解析组装。
DOI：
10.1186/s13059-023-03160-z
复制
发表时间：
2024-01-19
期刊：
影响因子：
12.3
通讯作者：
中科院分区：
文献类型：
--
作者：
马铃薯是世界主要粮食作物之一，和许多重要的农作物一样，它具有多倍体基因组。多倍体单倍型组装构成了一个主要的计算挑战。我们介绍了一种新的多倍体基因组组装策略，并提出了同源四倍体马铃薯品种Altus的组装方法。我们的方法使用来自后代群体的低深度测序数据来实现组装图上的染色体聚类和单倍型阶段化。我们的方法生成高质量的单个染色体组装，具有整个染色体臂的单倍型特定序列分辨率，并可应用于可获得后代集合的常见育种场景。网上版载有补充材料，可在10.1186/s13059-023-03160-z查阅。
Potato is one of the world’s major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses a major computational challenge. We introduce a novel strategy for the assembly of polyploid genomes and present an assembly of the autotetraploid potato cultivar Altus. Our method uses low-depth sequencing data from an offspring population to achieve chromosomal clustering and haplotype phasing on the assembly graph. Our approach generates high-quality assemblies of individual chromosomes with haplotype-specific sequence resolution of whole chromosome arms and can be applied in common breeding scenarios where collections of offspring are available. The online version contains supplementary material available at 10.1186/s13059-023-03160-z.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btac196
发表时间：
2022-05-13
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
通讯作者：
--
影响因子：
56.9
作者：
Nurk, Sergey;Koren, Sergey;Rhie, Arang;Rautiainen, Mikko;Bzikadze, Andrey V;Mikheenko, Alla;Vollger, Mitchell R;Altemose, Nicolas;Uralsky, Lev;Gershman, Ariel;Aganezov, Sergey;Hoyt, Savannah J;Diekhans, Mark;Logsdon, Glennis A;Alonge, Michael;Antonarakis, Stylianos E;Borchers, Matthew;Bouffard, Gerard G;Brooks, Shelise Y;Caldas, Gina V;Chen, Nae-Chyun;Cheng, Haoyu;Chin, Chen-Shan;Chow, William;de Lima, Leonardo G;Dishuck, Philip C;Durbin, Richard;Dvorkina, Tatiana;Fiddes, Ian T;Formenti, Giulio;Fulton, Robert S;Fungtammasan, Arkarachai;Garrison, Erik;Grady, Patrick G S;Graves-Lindsay, Tina A;Hall, Ira M;Hansen, Nancy F;Hartley, Gabrielle A;Haukness, Marina;Howe, Kerstin;Hunkapiller, Michael W;Jain, Chirag;Jain, Miten;Jarvis, Erich D;Kerpedjiev, Peter;Kirsche, Melanie;Kolmogorov, Mikhail;Korlach, Jonas;Kremitzki, Milinn;Li, Heng;Maduro, Valerie V;Marschall, Tobias;McCartney, Ann M;McDaniel, Jennifer;Miller, Danny E;Mullikin, James C;Myers, Eugene W;Olson, Nathan D;Paten, Benedict;Peluso, Paul;Pevzner, Pavel A;Porubsky, David;Potapova, Tamara;Rogaev, Evgeny I;Rosenfeld, Jeffrey A;Salzberg, Steven L;Schneider, Valerie A;Sedlazeck, Fritz J;Shafin, Kishwar;Shew, Colin J;Shumate, Alaina;Sims, Ying;Smit, Arian F A;Soto, Daniela C;Sovic, Ivan;Storer, Jessica M;Streets, Aaron;Sullivan, Beth A;Thibaud-Nissen, Francoise;Torrance, James;Wagner, Justin;Walenz, Brian P;Wenger, Aaron;Wood, Jonathan M D;Xiao, Chunlin;Yan, Stephanie M;Young, Alice C;Zarate, Samantha;Surti, Urvashi;McCoy, Rajiv C;Dennis, Megan Y;Alexandrov, Ivan A;Gerton, Jennifer L;O'Neill, Rachel J;Timp, Winston;Zook, Justin M;Schatz, Michael C;Eichler, Evan E;Miga, Karen H;Phillippy, Adam M
通讯作者：
Phillippy, Adam M
影响因子：
12.3
作者：
Rautiainen M;Marschall T
通讯作者：
Marschall T
影响因子：
9.2
作者：
Pham GM;Hamilton JP;Wood JC;Burke JT;Zhao H;Vaillancourt B;Ou S;Jiang J;Buell CR
通讯作者：
Buell CR
DOI：
10.1093/bioadv/vbad161
发表时间：
2023
期刊：
Bioinformatics advances
影响因子：
--
作者：
通讯作者：
--