Hao Weilong, Golding G Brian
Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
Genome Res. 2006 May;16(5):636-43. doi: 10.1101/gr.4746406.
Large-scale genome arrangement plays an important role in bacterial genome evolution. A substantial number of genes can be inserted into, deleted from, or rearranged within genomes during evolution. Detecting or inferring gene insertions/deletions is of interest because such information provides insights into bacterial genome evolution and speciation. However, efficient inference of genome events is difficult because genome comparisons alone do not generally supply enough information to distinguish insertions, deletions, and other rearrangements. In this study, homologous genes from the complete genomes of 13 closely related bacteria were examined. The presence or absence of genes from each genome was cataloged, and a maximum likelihood method was used to infer insertion/deletion rates according to the phylogenetic history of the taxa. It was found that whole gene insertions/deletions in genomes occur at rates comparable to or greater than the rate of nucleotide substitution and that higher insertion/deletion rates are often inferred to be present at the tips of the phylogeny with lower rates on more ancient interior branches. Recently transferred genes are under faster and relaxed evolution compared with more ancient genes. Together, this implies that many of the lineage-specific insertions are lost quickly during evolution and that perhaps a few of the genes inserted by lateral transfer are niche specific.
大规模基因组重排对细菌基因组进化起着重要作用。在进化过程中，大量基因可被插入基因组、从基因组中删除或在基因组内重排。检测或推断基因插入/缺失很有意义，因为此类信息能为细菌基因组进化和物种形成提供见解。然而，高效推断基因组事件很困难，因为仅靠基因组比较通常无法提供足够信息来区分插入、缺失和其他重排。在本研究中，对13种亲缘关系密切的细菌的完整基因组中的同源基因进行了检测。记录了每个基因组中基因的有无，并根据分类单元的系统发育历史，使用最大似然法推断插入/缺失率。研究发现，基因组中的全基因插入/缺失发生率与核苷酸替换率相当或更高，并且通常推断在系统发育树的末端具有较高的插入/缺失率，而在更古老的内部分支上发生率较低。与更古老的基因相比，近期转移的基因进化更快且更宽松。综合来看，这意味着许多谱系特异性插入在进化过程中很快丢失，并且可能少数通过横向转移插入的基因是特定于生态位的。
