Genome evolution at the genus level: Comparison of three complete genomes of hyperthermophilic Archaea
Genome evolution at the genus level: Comparison of three complete genomes of hyperthermophilic Archaea
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DOI：
10.1101/gr.gr1653r
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发表时间：
2001-06-01
期刊：
影响因子：
7
通讯作者：
Poch, O
中科院分区：
文献类型：
--
作者：
Lecompte, O;Ripp, R;Poch, O
我们已经比较了三个完整的基因组密切相关的超嗜热物种属于Pyrococcus属：Pyrococcus abyssi，Pyrococcus horikoshii和Pyrococcus furiosus。在基因组水平上，比较揭示了与介导DNA重组的通用元件的位置相关的四个区域的热球菌染色体之间的差异保守。这揭示了促进这些基因组可塑性的主要机制的相对贡献，即与复制末端相连的重排、插入序列介导的重组和tRNA基因内的DNA整合。这些机制的结合导致这些极端嗜热菌的基因组可塑性很高，至少与密切相关的细菌之间观察到的可塑性相当。在蛋白质组学水平上，三个Pyrococcus物种的比较揭示了特定的选择压力作用于它们的编码能力和进化速率。事实上，由于两个独立的方法，“互惠最佳命中”的方法和一个新的距离比分析，我们检测到错误的直系关系内的Pyrococcus谱系。这揭示了大量的差异增益和损失的基因，因为三个密切相关的物种的分歧。由此产生的多态性可能与这些自由生活的生物体对不同环境约束的适应有关。作为一个推论，我们描绘了一套由三个物种，即，基因，可能表征Pyrococcus属的orthopathic基因。在这个保守的核心中，深海拟杆菌和堀越拟杆菌之间的大多数共享蛋白质的氨基酸取代率是相等的，即使是快速进化的蛋白质也是如此。与此相反，强烈的差异存在的替代率之间观察到的P.furiosus相对于其他两个物种，这是不同意的分子钟假说。
We have compared three complete genomes of closely related hyperthermophilic species of Archaea belonging to the Pyrococcus genus: Pyrococcus abyssi, Pyrococcus horikoshii, and Pyrococcus furiosus. At the genomic level, the comparison reveals a differential conservation among Four regions of the Pyrococcus chromosomes correlated with the location of generic elements mediating DNA reorganization. This discloses the relative contribution of the major mechanisms that promote genomic plasticity in these Archaea, namely rearrangements linked to the replication terminus, insertion sequence-mediated recombinations, and DNA integration within tRNA genes. The combination of these mechanisms leads to a high level of genomic plasticity in these hyperthermophilic Archaea, at least comparable to the plasticity observed between closely related bacteria. At the proteomic level, the comparison of the three Pyrococcus species sheds light on specific selection pressures acting both on their coding capacities and evolutionary rates. Indeed, thanks to two independent methods, the "reciprocal best hits" approach and a new distance ratio analysis, we detect the false orthology relationships within the Pyrococcus lineage. This reveals a high amount of differential gains and losses of genes since the divergence of the three closely related species. The resulting polymorphism is probably linked to an adaptation of these free-living organisms to differential environmental constraints. As a corollary, we delineate the set of orthologous genes shared by the three species, that is, the genes that may characterize the Pyrococcus genus. In this conserved core, the amino acid substitution rate is equal between P. abyssi and P. horikoshii for most of their shared proteins, even for fast-evolving ones. In contrast, strong discrepancies exist among the substitution rates observed in P. furiosus relative to the two other species, which is in disagreement with the molecular clock hypothesis.