Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes
Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes
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DOI：
10.1128/jb.01237-08
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发表时间：
2009-01-01
影响因子：
3.2
通讯作者：
Koonin, Eugene V.
中科院分区：
文献类型：
--
作者：
Novichkov, Pavel S.;Wolf, Yuri I.;Koonin, Eugene V.
为了探索细菌和古菌的微进化趋势，我们构建了一个由41个可比对紧密基因组簇(ATGC)组成的数据集。我们发现，用非同义与同义替换率的中位数之比(dN/ds)来衡量蛋白质序列的净化选择压力是ATGC的稳定特性。与先前的发现一致，寄生细菌，尽管有时因基因丢失而导致基因组急剧萎缩，但通常受到相对较弱的净化选择，可能是由于相对较小的有效种群规模和频繁的瓶颈。然而，在任何一个ATGC中都没有发现由于强烈的选择压力而导致基因组流线型的证据。相反，基因组大小以及基因大小与选择压力之间存在显著的正相关，尽管各种自由生活的原核生物具有非常接近的选择压力，但几乎涵盖了整个基因组大小范围。此外，我们还研究了序列进化速度与其他基因组特征之间的关系。尽管在原核生物的进化过程中，基因序列的变化比蛋白质序列的变化快得多，但“后向距离”与氨基酸距离之间存在很强的正相关关系，这表明至少一些导致基因组重排的事件受到了与氨基酸序列进化相同类型的选择性约束。
In order to explore microevolutionary trends in bacteria and archaea, we constructed a data set of 41 alignable tight genome clusters (ATGCs). We show that the ratio of the medians of nonsynonymous to synonymous substitution rates (dN/dS) that is used as a measure of the purifying selection pressure on protein sequences is a stable characteristic of the ATGCs. In agreement with previous findings, parasitic bacteria, notwithstanding the sometimes dramatic genome shrinkage caused by gene loss, are typically subjected to relatively weak purifying selection, presumably owing to relatively small effective population sizes and frequent bottlenecks. However, no evidence of genome streamlining caused by strong selective pressure was found in any of the ATGCs. On the contrary, a significant positive correlation between the genome size, as well as gene size, and selective pressure was observed, although a variety of free-living prokaryotes with very close selective pressures span nearly the entire range of genome sizes. In addition, we examined the connections between the sequence evolution rate and other genomic features. Although gene order changes much faster than protein sequences during the evolution of prokaryotes, a strong positive correlation was observed between the "rear-rangement distance" and the amino acid distance, suggesting that at least some of the events leading to genome rearrangement are subjected to the same type of selective constraints as the evolution of amino acid sequences.