Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome.
Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome.
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支原体比较基因组学：保守必需基因和泛基因组多样性分析
DOI：
10.1371/journal.pone.0035698
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Xiao S
中科院分区：
文献类型：
--
作者：
Liu W;Fang L;Li M;Li S;Guo S;Luo R;Feng Z;Li B;Zhou Z;Shao G;Chen H;Xiao S
支原体是最小的自我复制有机体，代谢最少，基因组冗余也很少，预计它与维持细菌生命所需的最小基因集非常接近。本研究采用了20支原体基因组的比较进化分析，以获得对必需基因的更好理解。通过对支原体核心基因组的分析，我们最终揭示了支原体生存的保守必需基因集。进一步分析表明，核心基因组集与实验鉴定的必需基因具有许多共同特征。一些关键基因与DNA复制和修复有关，在转座子诱变研究中可能被破坏，它们可能对细菌的生存至关重要，特别是在长期的自然选择中。基于3355个同源群的系统发育重建允许对支原体菌株之间的系统发育相关性进行可靠的估计。为了更深入地了解分子进化在病原体适应宿主中的相对作用，我们还分析了特定位点和谱系的正选择压力。在物种的分化和相应谱系中检测到的正选择水平之间似乎有近似的相关性。
Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages.
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