Laboratoire d'Ecologie Alpine, Université Joseph Fourier, UMR-CNRS 5553, BP53 38041, Grenoble, France.
Mol Ecol Resour. 2014 Mar;14(2):411-8. doi: 10.1111/1755-0998.12189. Epub 2013 Nov 16.
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 study 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 analysed and 127,041 single-nucleotide polymorphisms identified. This contig data set will contribute to improving our understanding of the ecology of Arabis alpina, thus constituting an important resource for future ecological genomic studies.
高山植物Arabis alpina 是生态基因组学领域的新兴模式生物，非常适合鉴定在对比环境条件下参与局部适应的基因，而这一主题在分子水平上仍了解甚少。本研究使用下一代测序技术组装了Arabis alpina 基因组片段池。这些重叠群覆盖了 Arabis alpina 基因组的 172Mb（即基因组的 50%），并显示包含与 458 个 CEGMA 核心基因（核心真核生物基因作图方法）的 96%呈阳性匹配的序列，这是一组高度保守的真核生物基因。与近缘物种拟南芥的基因有 77%的高度核酸序列同一性的区域在不同的拟南芥基因功能类别中呈现出无偏的分布。该新资源通过重测序分析进行了测试，以鉴定多态性位点。成功分析了 16 个样本，鉴定出 127,041 个单核苷酸多态性。该重叠群数据集将有助于提高我们对 Arabis alpina 生态学的理解，因此构成了未来生态基因组学研究的重要资源。
