An Important Role for Purifying Selection in Archaeal Genome Evolution.
An Important Role for Purifying Selection in Archaeal Genome Evolution.
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纯化选择在古菌基因组进化中的重要作用
DOI：
10.1128/msystems.00112-17
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发表时间：
2017-09
期刊：
影响因子：
6.4
通讯作者：
Zhang Z
中科院分区：
文献类型：
--
作者：
Lyu Z;Li ZG;He F;Zhang Z
基因组复杂性的进化是生物学中的一个基本问题。真核生物基因组复杂性的一个标志是，较大的基因组往往具有更多的非编码序列，这在古细菌和细菌基因组中被认为是最小的。然而，我们发现古细菌基因组也具有这种真核生物特征，而细菌基因组则不具有。这可以从我们对遗传漂变的分析中预测出来，遗传漂变显示了在较大的古细菌基因组中宽松的纯化选择，这也是真核生物的特征。相比之下，细菌基因组的情况则相反。作为基因组进化的零假设，群体遗传学认为选择强度控制着基因组大小。通过遗传漂变过程，该理论预测，紧凑的基因组由强纯化选择维持，而复杂的基因组由弱纯化选择实现。它提供了一个统一的框架，解释了为什么原核生物的基因组比真核生物的基因组小得多。然而，最近的研究结果表明，更大的原核基因组似乎经历更强的纯化选择，表明纯化选择可能不会主导原核基因组的进化。由于古细菌基因组在这些研究中的代表性不足，因此可能没有必要将结论推广到古细菌和细菌基因组。在这项研究中，我们通过分别关注古细菌和细菌基因组来重新审视这一问题。我们发现，较大的细菌基因组确实经历了更强的纯化选择，但在古细菌基因组中观察到相反的情况。这一新发现将预测大型古细菌基因组中非编码序列的富集，这一点已通过编码密度分析得到证实。相反，编码密度保持稳定，无论细菌基因组大小。总之，这项研究表明，纯化选择可能在古细菌基因组进化中发挥更重要的作用，比以前假设的，这表明可能有一个重大的差异之间的进化制度的古细菌和细菌。基因组复杂性的进化是生物学中的一个基本问题。真核生物基因组复杂性的一个标志是，较大的基因组往往具有更多的非编码序列，这在古细菌和细菌基因组中被认为是最小的。然而，我们发现古细菌基因组也具有这种真核生物特征，而细菌基因组则不具有。这可以从我们对遗传漂变的分析中预测，遗传漂变显示了较大古细菌基因组中纯化选择的放松，这也是真核生物的特征。相比之下，细菌基因组的情况则相反。
The evolution of genome complexities is a fundamental question in biology. A hallmark of eukaryotic genome complexity is that larger genomes tend to have more noncoding sequences, which are believed to be minimal in archaeal and bacterial genomes. However, we found that archaeal genomes also possessed this eukaryotic feature while bacterial genomes did not. This could be predicted from our analysis of genetic drift, which showed relaxed purifying selection in larger archaeal genomes, also a eukaryotic feature. In contrast, the opposite was evident in bacterial genomes. ABSTRACT As the null hypothesis of genome evolution, population genetic theory suggests that selection strength controls genome size. Through the process of genetic drift, this theory predicts that compact genomes are maintained by strong purifying selection while complex genomes are enabled by weak purifying selection. It offers a unifying framework that explains why prokaryotic genomes are much smaller than their eukaryotic counterparts. However, recent findings suggest that bigger prokaryotic genomes appear to experience stronger purifying selection, indicating that purifying selection may not dominate prokaryotic genome evolution. Since archaeal genomes were underrepresented in those studies, generalization of the conclusions to both archaeal and bacterial genomes may not be warranted. In this study, we revisited this matter by focusing on archaeal and bacterial genomes separately. We found that bigger bacterial genomes indeed experienced stronger purifying selection, but the opposite was observed in archaeal genomes. This new finding would predict an enrichment of noncoding sequences in large archaeal genomes, which was confirmed by an analysis of coding density. In contrast, coding density remained stable regardless of bacterial genome size. In conclusion, this study suggests that purifying selection may play a more important role in archaeal genome evolution than previously hypothesized, indicating that there could be a major difference between the evolutionary regimes of Archaea and Bacteria. IMPORTANCE The evolution of genome complexity is a fundamental question in biology. A hallmark of eukaryotic genome complexity is that larger genomes tend to have more noncoding sequences, which are believed to be minimal in archaeal and bacterial genomes. However, we found that archaeal genomes also possessed this eukaryotic feature while bacterial genomes did not. This could be predicted from our analysis on genetic drift, which showed a relaxation of purifying selection in larger archaeal genomes, also a eukaryotic feature. In contrast, the opposite was evident in bacterial genomes.