Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries.
Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries.
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DOI：
10.1093/gigascience/giy053
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发表时间：
2018-05-01
期刊：
影响因子：
9.2
通讯作者：
Bevan MW
中科院分区：
文献类型：
--
作者：
Lu FH;McKenzie N;Kettleborough G;Heavens D;Clark MD;Bevan MW
非常大的、通常是多倍体的基因组的准确测序和组装仍然是一项具有挑战性的任务，限制了诸如植物育种等应用的远程序列信息和阶段性序列变异。15 GB的六倍体面包小麦(Triticum Aestivum)基因组测序尤其具有挑战性，最近有几种不同的方法产生了长距离组装。绘制和了解组装错误的类型对于优化未来的测序和组装方法以及比较基因组学很重要。在这里，我们使用一个38kb的Fosill跳跃文库来评估不同公开可用的小麦基因组组合的中长期顺序。对Fosill协议的修改产生了更长的Illumina序列，并实现了全面的基因组覆盖。对两个独立的基于细菌人工染色体(BAC)的染色体尺度组件、两个独立的Illumina全基因组猎枪组件以及一个杂交单分子实时(SMRT-PacBio)和短读(Illumina)组件进行了分析。我们使用Fosill配对映射揭示了令人惊讶的规模和多样性的差异，并验证了每个类别中的几个。此外，Fosill配对被用来支架整个基因组Illumina组装，导致N50值增加3倍。我们的分析使用一种独立的方法来验证不同的小麦基因组组合，结果表明，与基于BAC的染色体规模组合和SMRT-Illumina混合方法相比，仅基于Illumina序列的全基因组鸟枪组合在所有指标上都明显更准确。尽管目前的全基因组组装是相当准确和有用的，但还需要进一步的改进，以使用开源、计算高效和成本效益高的方法来生成小麦基因组的完整组装。
The accurate sequencing and assembly of very large, often polyploid, genomes remains a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15-Gb hexaploid bread wheat (Triticum aestivum) genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors are important for optimising future sequencing and assembly approaches and for comparative genomics. Here we use a Fosill 38-kb jumping library to assess medium and longer–range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent Bacterial Artificial Chromosome (BAC)-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a 3-fold increase in N50 values. Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient, and cost-effective methods.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
DOI：
10.1534/g3.117.040055
发表时间：
2017-05-05
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Crepeau MW;Langley CH;Stevens KA
通讯作者：
Stevens KA
影响因子：
11.6
作者：
Schmidt, Maximilian H. -W.;Vogel, Alexander;Usadel, Bjorn
通讯作者：
Usadel, Bjorn
影响因子：
48
作者：
Chin, Chen-Shan;Peluso, Paul;Schatz, Michael C.
通讯作者：
Schatz, Michael C.
影响因子：
56.9
作者：
Avni, Raz;Nave, Moran;Distelfeld, Assaf
通讯作者：
Distelfeld, Assaf