Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH 44555, USA.
DNA Res. 2013 Apr;20(2):163-71. doi: 10.1093/dnares/dss041. Epub 2013 Jan 7.
Recently, Brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. Using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (AS) events spanning across 2021 putatively assembled transcripts generated from 941 genes. Approximately, 6.3% of expressed genes are alternatively spliced in B. distachyon. We observed that a majority of the identified AS events were related to retained introns (55.5%), followed by alternative acceptor sites (16.7%). We also observed a low percentage of exon skipping (5.0%) and alternative donor site events (8.8%). The 'complex event' that consists of a combination of two or more basic splicing events accounted for ∼14.0%. Comparative AS transcript analysis revealed 163 and 39 homologous pairs between B. distachyon and Oryza sativa and between B. distachyon and Arabidopsis thaliana, respectively. In all, we found 16 AS transcripts to be conserved in all 3 species. AS events and related putative assembled transcripts annotation can be systematically browsed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/).
最近，短柄草已成为研究单子叶禾本科植物和谷类作物的模式植物。我们利用组装的表达转录序列，并将其随后映射到相应的基因组，鉴定了 1219 个可变剪接（AS）事件，跨越了 941 个基因中 2021 个推测组装的转录本。大约 6.3%的表达基因在短柄草中存在可变剪接。我们观察到，大多数鉴定出的 AS 事件与内含子保留（55.5%）有关，其次是供体和受体剪接位点的替换（16.7%）。我们还观察到外显子跳跃（5.0%）和供体剪接位点替换（8.8%）的比例较低。由两种或多种基本剪接事件组合而成的“复杂事件”占∼14.0%。比较 AS 转录分析显示，在短柄草和水稻之间以及短柄草和拟南芥之间分别有 163 和 39 对同源对。总的来说，我们发现 16 个 AS 转录本在这 3 个物种中都是保守的。AS 事件和相关的推测组装转录本注释可以在植物可变剪接数据库（http://proteomics.ysu.edu/altsplice/plant/）中系统浏览。
