Highly contiguous assemblies of 101 drosophilid genomes.
Highly contiguous assemblies of 101 drosophilid genomes.
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DOI：
10.7554/elife.66405
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发表时间：
2021-07-19
期刊：
影响因子：
7.7
通讯作者：
Petrov DA
中科院分区：
文献类型：
--
作者：
Kim BY;Wang JR;Miller DE;Barmina O;Delaney E;Thompson A;Comeault AA;Peede D;D'Agostino ERR;Pelaez J;Aguilar JM;Haji D;Matsunaga T;Armstrong EE;Zych M;Ogawa Y;Stamenković-Radak M;Jelić M;Veselinović MS;Tanasković M;Erić P;Gao JJ;Katoh TK;Toda MJ;Watabe H;Watada M;Davis JS;Moyle LC;Manoli G;Bertolini E;Košťál V;Hawley RS;Takahashi A;Jones CD;Price DK;Whiteman N;Kopp A;Matute DR;Petrov DA
对黑腹果蝇和果蝇属中相关物种的100多年研究促进了遗传学、基因组学和进化方面的关键发现。虽然高质量的基因组组装存在于这个组中的几个物种，但它们只包含该属的一小部分。长读段测序的最新进展允许高效地产生数十个甚至数百个物种的高质量基因组组装。在这里，我们利用牛津纳米孔测序建立一个开放的社区资源的基因组组件的101行93果蝇物种，包括14个物种组和35个亚组。基因组是高度连续和完整的，平均重叠群N50为10.5 Mb，在97/101组装中的BUSCO完整性大于97%。我们表明，基于纳米孔的组件是高度准确的编码区，特别是在编码插入和缺失。这些组件，沿着详细的实验室协议和组装管道，作为公共资源发布，并将作为解决数百个物种规模的遗传学，生态学和进化的广泛问题的起点。
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.