New maximum likelihood estimators for eukaryotic intron evolution
New maximum likelihood estimators for eukaryotic intron evolution
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DOI：
10.1371/journal.pcbi.0010079
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发表时间：
2005-12-01
影响因子：
4.3
通讯作者：
Kenmochi, Naoya
中科院分区：
文献类型：
--
作者：
Nguyen, Hung D.;Yoshihama, Maki;Kenmochi, Naoya
剪接体内含子的进化仍然知之甚少。虽然许多方法已经被用来从内含子位置守恒的模式来推断内含子的进化，但迄今为止的结果是矛盾的。在本文中，我们使用一种新的最大似然方法来解决这个问题，该方法可以估计内含子插入目标位点的频率，以及内含子的获得和丢失率。我们分析了来自7种真核生物的684组同源基因保守区10044个内含子（7221个内含子位置）的模式。我们确定平均每11.86个碱基对（bp）有一个目标位点（95%置信区间，9.27至14.39 bp）。此外，我们的结果表明：(i)总体内含子增益为；比内含子损失大25%，尽管具体模式随时间和谱系而变化；（ii）平行收益占；共有内含子位置的18.5%；（三）损失核算后的重新取得；占所有内含子位置的0.5%我们的结果应该有助于解决长期存在的问题，推断剪接体内含子的进化。
The evolution of spliceosomal introns remains poorly understood. Although many approaches have been used to infer intron evolution from the patterns of intron position conservation, the results to date have been contradictory. In this paper, we address the problem using a novel maximum likelihood method, which allows estimation of the frequency of intron insertion target sites, together with the rates of intron gain and loss. We analyzed the pattern of 10,044 introns (7,221 intron positions) in the conserved regions of 684 sets of orthologs from seven eukaryotes. We determined that there is an average of one target site per 11.86 base pairs (bp) (95% confidence interval, 9.27 to 14.39 bp). In addition, our results showed that: (i) overall intron gains are; 25% greater than intron losses, although specific patterns vary with time and lineage; (ii) parallel gains account for; 18.5% of shared intron positions; and (iii) reacquisition following loss accounts for; 0.5% of all intron positions. Our results should assist in resolving the long-standing problem of inferring the evolution of spliceosomal introns.