Long-read sequence assembly: a technical evaluation in barley.
Long-read sequence assembly: a technical evaluation in barley.
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DOI：
10.1093/plcell/koab077
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发表时间：
2021-07-19
期刊：
影响因子：
--
通讯作者：
Stein N
中科院分区：
文献类型：
--
作者：
Mascher M;Wicker T;Jenkins J;Plott C;Lux T;Koh CS;Ens J;Gundlach H;Boston LB;Tulpová Z;Holden S;Hernández-Pinzón I;Scholz U;Mayer KFX;Spannagl M;Pozniak CJ;Sharpe AG;Šimková H;Moscou MJ;Grimwood J;Schmutz J;Stein N
大型和重复序列丰富的植物基因组的序列组装一直是具有挑战性的，需要大量的计算资源，往往是几个互补的序列组装和基因组作图方法。最近在PacBio平台上通过循环共识测序（CCS）开发的快速准确的长读段测序可能会大大增加植物泛基因组项目的范围。在这里，我们比较了目前的长读测序平台的能力，迅速产生连续的序列组装在大麦（大麦）的泛基因组研究。大多数长读段组装明显上级基于短读段的当前大麦参考序列。来自准确长读段的组装在大多数指标中表现出色，但CCS方法是组装数十个大麦基因组的最具成本效益的策略。下采样分析表明，20倍的CCS覆盖率可以产生非常好的序列组装，而即使是5倍的CCS数据也可以捕获大多数基因的完整序列。我们提出了一个更新的参考基因组组装大麦与近完整的重复丰富的基因间空间的代表性。长读段组装可以构建一个物种的多个基因组的准确和完整的序列，以建立小麦族作物及其野生近缘种的泛基因组基础设施。从准确的长读段组装了大大改进的大麦参考基因组序列。
Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives. A greatly improved reference genome sequence of barley was assembled from accurate long reads.
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影响因子：
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作者：
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通讯作者：
Stanke, Mario
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3.1
作者：
DVORAK, J;MCGUIRE, PE;CASSIDY, B
通讯作者：
CASSIDY, B
影响因子：
48
作者：
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通讯作者：
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