Reductive genome evolution from the mother of Rickettsia

被引:135
作者
Blanc, Guillaume [1 ]
Ogata, Hiroyuki
Robert, Catherine
Audic, Stephane
Suhre, Karsten
Vestris, Guy
Claverie, Jean-Michel
Raoult, Didier
机构
[1] Inst Biol Struct & Microbiol, Struct & Genom Informat Lab, Marseille, France
[2] Fac Med, Unite Rickettsies, Marseille, France
来源
PLOS GENETICS | 2007年 / 3卷 / 01期
关键词
D O I
10.1371/journal.pgen.0030014
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
The Rickettsia genus is a group of obligate intracellular alpha-proteobacteria representing a paradigm of reductive evolution. Here, we investigate the evolutionary processes that shaped the genomes of the genus. The reconstruction of ancestral genomes indicates that their last common ancestor contained more genes, but already possessed most traits associated with cellular parasitism. The differences in gene repertoires across modern Rickettsia are mainly the result of differential gene losses from the ancestor. We demonstrate using computer simulation that the propensity of loss was variable across genes during this process. We also analyzed the ratio of nonsynonymous to synonymous changes (Ka/Ks) calculated as an average over large sets of genes to assay the strength of selection acting on the genomes of Rickettsia, Anaplasmataceae, and free-living gamma-proteobacteria. As a general trend, Ka/Ks were found to decrease with increasing divergence between genomes. The high Ka/Ks for closely related genomes are probably due to a lag in the removal of slightly deleterious nonsynonymous mutations by natural selection. Interestingly, we also observed a decrease of the rate of gene loss with increasing divergence, suggesting a similar lag in the removal of slightly deleterious pseudogene alleles. For larger divergence (Ks > 0.2), Ka/Ks converge toward similar values indicating that the levels of selection are roughly equivalent between intracellular alpha-proteobacteria and their free-living relatives. This contrasts with the view that obligate endocellular microorganisms tend to evolve faster as a consequence of reduced effectiveness of selection, and suggests a major role of enhanced background mutation rates on the fast protein divergence in the obligate intracellular alpha-proteobacteria.
引用
收藏
页码:0103 / 0114
页数:12
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