Ortutay Csaba, Gáspári Zoltán, Tóth Gábor, Jáger Edit, Vida Gábor, Orosz László, Vellai Tibor
Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary.
J Mol Evol. 2003 Dec;57(6):672-80. doi: 10.1007/s00239-003-2517-3.
Horizontal gene transfer (HGT), a process through which genomes acquire sequences from distantly related organisms, is believed to be a major source of genetic diversity in bacteria. A central question concerning the impact of HGT on bacterial genome evolution is the proportion of horizontally transferred sequences within genomes. This issue, however, remains unresolved because the various methods developed to detect potential HGT events identify different sets of genes. The present-day consensus is that phylogenetic analysis of individual genes is still the most objective and accurate approach for determining the occurrence and directionality of HGT. Here we present a genome-scale phylogenetic analysis of protein-encoding genes from five closely related Chlamydia, identifying a reliable set of sequences that have arisen via HGT since the divergence of the Chlamydia lineage. According to our knowledge, this is the first systematic phylogenetic inference-based attempt to establish a reliable set of acquired genes in a bacterial genome. Although Chlamydia are obligate intracellular parasites of higher eukaryotes, and thus suspected to be isolated from HGT more than the free-living species, our results show that their diversification has involved the introduction of foreign sequences into their genome. Furthermore, we also identified a complete set of genes that have undergone deletion, duplication, or rearrangement during this evolutionary period leading to the radiation of Chlamydia species. Our analysis may provide a deeper insight into how these medically important pathogens emerged and evolved from a common ancestor.
水平基因转移（HGT）是基因组从远缘生物体获取序列的过程，被认为是细菌遗传多样性的主要来源。一个关于HGT对细菌基因组进化影响的核心问题是基因组内水平转移序列的比例。然而，这个问题仍未解决，因为为检测潜在HGT事件而开发的各种方法识别出不同的基因集。目前的共识是，对单个基因进行系统发育分析仍然是确定HGT发生和方向性的最客观、准确的方法。在此，我们对五个密切相关的衣原体中编码蛋白质的基因进行了全基因组规模的系统发育分析，确定了一组自衣原体谱系分化以来通过HGT产生的可靠序列。据我们所知，这是首次基于系统发育推断在细菌基因组中建立一组可靠的获得性基因的系统性尝试。虽然衣原体是高等真核生物的专性细胞内寄生虫，因此比自由生活的物种更有可能与HGT隔离，但我们的结果表明，它们的多样化涉及将外来序列引入其基因组。此外，我们还确定了在导致衣原体物种辐射的进化时期内经历了缺失、重复或重排的一整套基因。我们的分析可能会更深入地了解这些医学上重要的病原体是如何从共同祖先中出现和进化的。
