Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.
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DOI：
10.1111/tpj.12294
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发表时间：
2013-11
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;Richmond TA;Gerhardt DJ;Himmelbach A;Clissold L;Sampath D;Ayling S;Steuernagel B;Pfeifer M;D'Ascenzo M;Akhunov ED;Hedley PE;Gonzales AM;Morrell PL;Kilian B;Blattner FR;Scholz U;Mayer KF;Flavell AJ;Muehlbauer GJ;Waugh R;Jeddeloh JA;Stein N
大麦（Hordeum vulgare）基因组辅助研究的先进资源，包括全基因组霰弹枪组装和综合物理图谱最近已经可用。这使得旨在评估遗传多样性或通过全基因组重测序和计算机变异检测分离单个基因的研究成为可能。然而，考虑到大麦基因组的5gb大小，这种方法仍然很昂贵。mrna编码外显子组的靶向测序将大麦基因组的复杂性降低了50倍以上，从而大大减少了繁重的测序和分析负担。我们开发并使用了一个基于溶液内杂交的序列捕获平台，选择性地富集61.6兆碱基编码序列目标，该目标包括来自栽培品种Morex基因组组装的预测基因，以及公开可用的全长cdna和从头组装的RNA-Seq共识序列。该平台为栽培大麦和相关物种提供了高度特异性的捕获，具有大量可重复的目标外显子富集。我们表明，这种外显子组捕获平台为更广泛、更深入地了解大麦基因组mrna编码部分的自然变异提供了一条清晰的途径，从而为测序图谱和遗传多样性分析等应用提供了宝贵的资源。
Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole-genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the mRNA-coding exome reduces barley genomic complexity more than 50-fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in-solution hybridization-based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar Morex as well as publicly available full-length cDNAs and de novo assembled RNA-Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the mRNA-coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping-by-sequencing and genetic diversity analyzes.
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