Intron loss and gain in Drosophila
Intron loss and gain in Drosophila
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DOI：
10.1093/molbev/msm235
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发表时间：
2007-12-01
影响因子：
10.7
通讯作者：
Majewski, Jacek
中科院分区：
文献类型：
--
作者：
Coulombe-Huntington, Jasmin;Majewski, Jacek
尽管内含子在近30年前首次被发现，但它们的进化起源仍然难以捉摸。在这项工作中，我们使用多物种全基因组比对将黑腹果蝇内含子映射到其他10个完全测序的果蝇基因组上。我们发现了1,944个在一个或多个物种中缺失内含子的位点。我们表明，对于大多数（> 80%）的这些情况下，没有剩余的内含子序列或任何缺失的外显子序列，表明确切的内含子丢失或获得事件。我们使用简约法将这些差异分类为1，754个内含子丢失事件和213个增益事件。我们发现，丢失和获得的内含子显着短于平均水平，两侧的外显子长于平均水平。它们还显示出相当不同的相位分布，并显示出5'剪接位点与其3'配偶体剪接位点之间大于平均的相似性。在一个或多个物种中丢失的内含子比其他内含子进化得更快，出现在进化缓慢的基因中，并且比独立的单个丢失更经常地被发现彼此相邻。我们的研究结果支持内含子丢失的cDNA重组机制，表明选择压力影响位点特异性丢失率，并最终表明，内含子增益发生在果蝇谱系内，巩固了“内含子中间”的假设，并提供了一些提示增益机制。
Although introns were first discovered almost 30 years ago, their evolutionary origin remains elusive. In this work, we used multispecies whole-genome alignments to map Drosophila melanogaster introns onto 10 other fully sequenced Drosophila genomes. We were able to find 1,944 sites where an intron was missing in one or more species. We show that for most (> 80%) of these cases, there is no leftover intronic sequence or any missing exonic sequence, indicating exact intron loss or gain events. We used parsimony to classify these differences as 1,754 intron loss events and 213 gain events. We show that lost and gained introns are significantly shorter than average and flanked by longer than average exons. They also display quite distinct phase distributions and show greater than average similarity between the 5' splice site and its 3' partner splice site. Introns that have been lost in one or more species evolve faster than other introns, occur in slowly evolving genes, and are found adjacent to each other more often than would be expected for independent single losses. Our results support the cDNA recombination mechanism of intron loss, suggest that selective pressures affect site-specific loss rates, and show conclusively that intron gain has occurred within the Drosophila lineage, solidifying the "introns-middle" hypothesis and providing some hints about the gain mechanism.