Development of an Arabis alpina genomic contig sequence dataset and application to single nucleotide polymorphisms discovery

The alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well-suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This paper presents the assembly of a pool of A. alpina genomic fragments using Next Generation Sequencing technologies. These contigs cover 172 Mb of the A. alpina genome (i.e. 50% of the genome) and were shown to contain sequences giving positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic Genes Mapping Approach), a set of highly conserved eukaryotic genes. Regions presenting high nucleic sequence identity with 77% of the close relative Arabidopsis thaliana's genes were found, with an unbiased distribution across the different functional categories of A. thaliana genes. This new resource was tested using a resequencing assay to identify polymorphic sites. Sixteen samples were successfully analyzed and 127,041 S...高山南芥（Arabis alpina）是生态基因组学领域的新兴模式生物，其非常适用于识别差异化环境条件下参与局部适应的基因——这一主题在分子层面仍有待深入阐释。本研究采用下一代测序（Next Generation Sequencing）技术完成了高山南芥基因组片段池的组装。该组装得到的重叠群（contig）覆盖高山南芥基因组172 Mb的序列，约占其全基因组的50%；经检测，这些序列可与CEGMA（Core Eukaryotic Genes Mapping Approach，真核生物核心基因定位方法）的458个核心基因中的96%获得阳性比对结果。研究还发现，77%的近缘物种拟南芥（Arabidopsis thaliana）基因可与该组装序列找到高核酸序列同源性区域，且此类同源区域在拟南芥各类功能基因类别中分布无偏倚。本新型基因组资源通过重测序试验开展性能验证，以筛选多态性位点，共成功分析16份样本，鉴定得到127041个S……