Patterns of intron gain and conservation in eukaryotic genes
Patterns of intron gain and conservation in eukaryotic genes
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DOI：
10.1186/1471-2148-7-192
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发表时间：
2007-10-12
影响因子：
3.4
通讯作者：
Koonin, Eugene V.
中科院分区：
文献类型：
--
作者：
Carmel, Liran;Rogozin, Igor B.;Koonin, Eugene V.
背景：编码蛋白质的基因中存在内含子是真核生物基因组组织的普遍特征，而多细胞真核生物的基因中通常含有多个内含子，其中很大一部分内含子在遥远的类群中具有相同的位置，如植物和动物。根据使用的方法和数据集的不同，研究人员对来自遥远的真核生物的同源基因中共享内含子比例较高的原因得出了相反的结论。一些研究得出结论，共享内含子的位置几乎完全反映了一种显著的进化保守，而另一些研究则将其归因于内含子的平行获得。为了解决这些矛盾，使用一个最大限度地依赖于任意假设的模型来分析内含子的进化是至关重要的。结果：我们建立了一个进化的概率模型，该模型允许内含子在系统发育树的分支、单个基因和单个位点上的增减率的变异性。将该模型应用于一组扩展的保守真核基因，我们发现平均而言，平行增益仅占共享内含子位置的8%。然而，在真核生物的系统发育树上，并行增益的分布是高度不均匀的。实际上，在密切相关的谱系中没有平行的遗传，而对于遥远的谱系，例如动物和植物，平行的遗传似乎贡献了高达20%的共享内含子位置。根据这些发现，我们估计了祖先内含子很有可能被保留在现有的基因组中，相反，自真核进化的早期阶段以来，相当一部分现有的内含子一直保持着它们的位置。此外，可用于内含子插入的位点密度估计约为七分之一的碱基。结论：我们获得了对不同进化距离的真核生物物种之间观察到的内含子位置共享的贡献的稳健估计。结果表明，尽管在整个系统发育树中，平行收益的贡献有所不同，但内含子位置共享的高水平主要是由于进化保守。因此，在数亿年的进化过程中，许多内含子似乎保持在相同的位置。这与最近观察到的基因内含子获得率和编码序列进化速率之间的负相关是一致的，这表明至少有一些内含子是功能相关的。
Background: The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction of which share position in distant taxa, such as plants and animals. Depending on the methods and data sets used, researchers have reached opposite conclusions on the causes of the high fraction of shared introns in orthologous genes from distant eukaryotes. Some studies conclude that shared intron positions reflect, almost entirely, a remarkable evolutionary conservation, whereas others attribute it to parallel gain of introns. To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions.Results: We developed a probabilistic model of evolution that allows for variability of intron gain and loss rates over branches of the phylogenetic tree, individual genes, and individual sites. Applying this model to an extended set of conserved eukaryotic genes, we find that parallel gain, on average, accounts for only similar to 8% of the shared intron positions. However, the distribution of parallel gains over the phylogenetic tree of eukaryotes is highly non-uniform. There are, practically, no parallel gains in closely related lineages, whereas for distant lineages, such as animals and plants, parallel gains appear to contribute up to 20% of the shared intron positions. In accord with these findings, we estimated that ancestral introns have a high probability to be retained in extant genomes, and conversely, that a substantial fraction of extant introns have retained their positions since the early stages of eukaryotic evolution. In addition, the density of sites that are available for intron insertion is estimated to be, approximately, one in seven basepairs.Conclusion: We obtained robust estimates of the contribution of parallel gain to the observed sharing of intron positions between eukaryotic species separated by different evolutionary distances. The results indicate that, although the contribution of parallel gains varies across the phylogenetic tree, the high level of intron position sharing is due, primarily, to evolutionary conservation. Accordingly, numerous introns appear to persist in the same position over hundreds of millions of years of evolution. This is compatible with recent observations of a negative correlation between the rate of intron gain and coding sequence evolution rate of a gene, suggesting that at least some of the introns are functionally relevant.