More effective purifying selection on RNA viruses than in DNA viruses
More effective purifying selection on RNA viruses than in DNA viruses
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DOI：
10.1016/j.gene.2007.09.013
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发表时间：
2007-12-01
期刊：
影响因子：
3.5
通讯作者：
Hughes, Mary Ann K.
中科院分区：
文献类型：
--
作者：
Hughes, Austin L.;Hughes, Mary Ann K.
对 222 个独立病毒序列数据集中的核苷酸多样性模式的分析显示了纯化选择的普遍性。尽管RNA病毒的突变率较高，但我们的分析揭示了RNA病毒比DNA病毒有更强的纯化选择作用的证据。 RNA病毒中非同义核苷酸多样性与同义核苷酸多样性的比率显着低于DNA病毒，这表明前者的非同义突变去除率（相对于突变率）高于后者。此外，测量罕见多态性发生率的统计数据显示，RNA病毒中的罕见非同义多态性明显多于DNA病毒，但同义多态性方面没有差异。由于罕见的非同义多态性可能会受到纯化选择的作用以消除它们，因此这一结果意味着 RNA 病毒中持续纯化选择的特征比 DNA 病毒更强。在 DNA 病毒和 RNA 病毒的数据集中，我们发现非同义和同义核苷酸多样性之间存在负异速关系；换句话说，非同义核苷酸多样性随着同义核苷酸多样性以低于线性的速度增加。这些发现最容易通过轻微有害突变的发生来解释。负异速生长在 RNA 病毒中比在 DNA 病毒中更明显这一事实提供了额外的证据，证明前者的纯化选择比后者更有效。 (C) 2007 Elsevier B.V. 保留所有权利。
Analysis of the pattern of nucleotide diversity in 222 independent viral sequence datasets showed the prevalence of purifying selection. In spite of the higher mutation rate of RNA viruses, our analyses revealed stronger evidence of the action of purifying selection in RNA viruses than in DNA viruses. The ratio of nonsynonymous to synonymous nucleotide diversity was significantly lower in RNA viruses than in DNA viruses, indicating that nonsynonymous mutations have been removed at a greater rate (relative to the mutation rate) in the former than in the latter. Moreover, statistics that measure the occurrence of rare polymorphisms revealed significantly a greater excess of rare nonsynonymous polymorphisms in RNA viruses than in DNA viruses but no difference with respect to synonymous polymorphisms. Since rare nonsynonymous polymorphisms are likely to be undergoing the effects of purifying selection acting to eliminate them, this result implies a stronger signature of ongoing purifying selection in RNA viruses than in DNA viruses. Across datasets from both DNA viruses and RNA viruses, we found a negatively allometric relationship between nonsynonymous and synonymous nucleotide diversity; in other words, nonsynonymous nucleotide diversity increased with synonymous nucleotide diversity at a less than linear rate. These findings are most easily explained by the occurrence of slightly deleterious mutations. The fact that the negative allometry was more pronounced in RNA viruses than in DNA viruses provided additional evidence that purifying selection is more effective in the former than in the latter. (C) 2007 Elsevier B.V. All rights reserved.