University of North Carolina, Chapel Hill, NC, USA.
Brief Bioinform. 2009 Nov;10(6):631-44. doi: 10.1093/bib/bbp051.
The residence of spliceosomal introns within protein-coding genes can fluctuate over time, with genes gaining, losing or conserving introns in a complex process that is not entirely understood. One approach for studying intron evolution is to compare introns with respect to position and type within closely related genes. Here, we describe new, freely available software called Common Introns Within Orthologous Genes (CIWOG), available at http://ciwog.gdcb.iastate.edu/, which detects common introns in protein-coding genes based on position and sequence conservation in the corresponding protein alignments. CIWOG provides dynamic web displays that facilitate detailed intron studies within orthologous genes. User-supplied options control how introns are clustered into sets of common introns. CIWOG also identifies special classes of introns, in particular those with GC- or U12-type donor sites, which enables analyses of these introns in relation to their counterparts in the other genes in orthologous groups. The software is demonstrated with application to a comprehensive study of eight plant transcriptomes. Three specific examples are discussed: intron class conversion from GT- to GC-donor-type introns in monocots, plant U12-type intron conservation and a global analysis of intron evolution across the eight plant species.
剪接体内含子在蛋白质编码基因中的位置会随时间发生波动，基因通过一个复杂的过程获得、丢失或保留内含子，而这个过程并不完全清楚。研究内含子进化的一种方法是根据密切相关基因中内含子的位置和类型进行比较。这里，我们描述了一种新的、免费的软件，称为“直系同源基因中的共有内含子（Common Introns Within Orthologous Genes，CIWOG）”，可在 http://ciwog.gdcb.iastate.edu/ 获取，它基于相应蛋白质比对中的位置和序列保守性，检测蛋白质编码基因中的共有内含子。CIWOG 提供动态的网络显示，便于在直系同源基因内进行详细的内含子研究。用户提供的选项控制如何将内含子聚类为共有内含子集。CIWOG 还识别特殊类别的内含子，特别是具有 GC 或 U12 型供体位点的内含子，这使得能够分析这些内含子与其在直系同源基因中对应物的关系。该软件通过对八个植物转录组的综合研究进行了演示。讨论了三个具体示例：单子叶植物 GT- 到 GC- 供体型内含子的内含子类别转换、植物 U12 型内含子的保守性以及八个植物物种中内含子进化的全局分析。
