The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
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DOI：
10.1073/pnas.0901808106
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发表时间：
2009-05-05
影响因子：
11.1
通讯作者：
Lipman, David J.
中科院分区：
文献类型：
--
作者：
Wolf, Yuri I.;Novichkov, Pavel S.;Lipman, David J.
生物体中蛋白质编码基因的进化速率跨越大约3个数量级，并且在从原核生物到哺乳动物的各种物种中显示出普遍的近似对数正态分布。这种普遍分布意味着一个稳态过程，在获得的基因和丢失的基因之间，进化速率的分布是相同的。在基因丢失倾向（PGL）分布恒定的单一假设下，建立了这一过程的数学模型。该模型预测，不同年龄的基因，即在不同系统发育深度可检测到同源物的基因，在与PGL相关的那些变量中存在显著差异。我们通过计算将来自人类、苍蝇和曲霉菌的蛋白质编码基因划分为不同的年龄组，并表明不同年龄的基因保持了进化速率的普遍对数正态分布，在“进化者”类中向更高的速率转变，但也有大量的重叠。唯一的例外是人类灵长类特有的基因，它们显示出快速进化的基因的沉重尾巴，这可能是由于基因注释人工制品。正如预测的那样，基因年龄组与PGL相关的特征不同。与“基因”（例如，哺乳动物特有的人类基因），“老”基因（例如，真核生物特异性的）平均更长，以更高的水平表达，具有更高的内含子密度，在短时间尺度上进化较慢，并且经受更强的纯化选择。因此，基因组进化符合一个简单的模型，具有近似均匀的基因获得和丢失率，而没有基因组创新的大爆发。
The evolutionary rates of protein-coding genes in an organism span, approximately, 3 orders of magnitude and show a universal, approximately log-normal distribution in a broad variety of species from prokaryotes to mammals. This universal distribution implies a steady-state process, with identical distributions of evolutionary rates among genes that are gained and genes that are lost. A mathematical model of such process is developed under the single assumption of the constancy of the distributions of the propensities for gene loss (PGL). This model predicts that genes of different ages, that is, genes with homologs detectable at different phylogenetic depths, substantially differ in those variables that correlate with PGL. We computationally partition protein-coding genes from humans, flies, and Aspergillus fungus into age classes, and show that genes of different ages retain the universal log-normal distribution of evolutionary rates, with a shift toward higher rates in "younger'' classes but also with a substantial overlap. The only exception involves human primate-specific genes that show a heavy tail of rapidly evolving genes, probably owing to gene annotation artifacts. As predicted, the gene age classes differ in characteristics correlated with PGL. Compared with "young'' genes (e.g., mammal-specific human ones), "old'' genes (e.g., eukaryote-specific), on average, are longer, are expressed at a higher level, possess a higher intron density, evolve slower on the short time scale, and are subject to stronger purifying selection. Thus, genome evolution fits a simple model with approximately uniform rates of gene gain and loss, without major bursts of genomic innovation.