Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines
Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines
复制标题
DOI：
10.1111/tpj.12569
复制
发表时间：
2014-08-01
期刊：
影响因子：
7.2
通讯作者：
Vogel, John P.
中科院分区：
文献类型：
--
作者：
Gordon, Sean P.;Priest, Henry;Vogel, John P.
短柱草是一年生小草，已被用作牧草的模式。它的小基因组、高质量的参考基因组、大量的种质收集和自交性质使其成为研究自然变异的极佳对象。我们对6个不同的品系进行了测序，以确定一套全面的多态，并分析它们的分布及其与基因表达的一致性。采用多种方法和对照方法鉴定其多态性并验证其质量。在对照和模拟干旱胁迫条件下的mRNA-Seq实验中，鉴定出300个基因具有依赖于基因型的处理反应。我们发现，大规模的序列变异与数百个基因的表达变化具有极高的一致性，其中包括许多与基因型相关的治疗反应。我们为最分化的品系生成了一个深层的mRNA-Seq数据集，并创建了一个从头开始的转录组组件。这导致发现了2400个以前没有注释的转录本和数百个不存在于参考基因组中的基因。我们建立了一个公共数据库，用于可视化和研究这些广泛使用的自交系之间的序列变异。
Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.