Homologous Recombination in Agrobacterium: Potential Implications for the Genomic Species Concept in Bacteria
Homologous Recombination in Agrobacterium: Potential Implications for the Genomic Species Concept in Bacteria
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DOI：
10.1093/molbev/msn236
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发表时间：
2009-01-01
影响因子：
10.7
通讯作者：
Nesme, Xavier
中科院分区：
文献类型：
--
作者：
Costechareyre, Denis;Bertolla, Franck;Nesme, Xavier
根据目前的分类学规则，真正的细菌物种是以其成员的基因组相似性为特征的基因组物种。有人提出，这种集群的基因组凝聚力可能与性隔离有关，性隔离限制了过于分化的细菌之间的基因流动。同源重组是研究最多的机制之一，负责这种遗传隔离。之前对几种细菌模型的研究表明，重组频率随着DNA序列差异的增加而呈指数级下降。在本研究中，我们调查了这种关系在根癌农杆菌物种复合体，这使我们能够集中在基因组物种的遗传边界附近的序列分歧。我们观察到重组频率对DNA分歧的敏感性符合对数线性函数，直到大约10%的序列分歧。结果清楚地表明，在序列趋异分布显示出描绘基因组物种的“缺口”的点处，重组频率没有急剧下降。在同配条件下的重组频率相对于异配条件下的重组频率的比率，即性隔离，被发现从一个物种内最远的菌株之间的8降低到最密切相关的物种之间的9，相应地从4.3%增加到6.4%的标记基因chvA的错配。这意味着，在物种边界的两个边缘，重组事件的重组频率仅降低了1.13倍。因此，从这次调查的结果，我们得出结论，-025 EFat至少在这个分类群-025 EF性隔离的基础上同源重组可能不高，足以强烈阻碍物种之间的基因流相比，基因流之间的远亲成员相同的物种。用于定义细菌种属的70%相对结合率截止值可能仅与同源重组频率的轻微下降相关。因此，序列多样性，作为重组效率的机制因素（如在实验室中测定的），似乎在细菌物种的遗传凝聚力中起很小的作用，因此，原核生物的基因组物种定义与真核生物的生物物种概念肯定是不一致的。
According to current taxonomical rules, a bona fide bacterial species is a genomic species characterized by the genomic similarity of its members. It has been proposed that the genomic cohesion of such clusters may be related to sexual isolation, which limits gene flow between too divergent bacteria. Homologous recombination is one of the most studied mechanisms responsible for this genetic isolation. Previous studies on several bacterial models showed that recombination frequencies decreased exponentially with increasing DNA sequence divergence. In the present study, we investigated this relationship in the Agrobacterium tumefaciens species complex, which allowed us to focus on sequence divergence in the vicinity of the genetic boundaries of genomic species. We observed that the sensitivity of the recombination frequency to DNA divergence fitted a log-linear function until approximately 10% sequence divergence. The results clearly revealed that there was no sharp drop in recombination frequencies at the point where the sequence divergence distribution showed a "gap" delineating genomic species. The ratio of the recombination frequency in homogamic conditions relative to this frequency in heterogamic conditions, that is, sexual isolation, was found to decrease from 8 between the most distant strains within a species to 9 between the most closely related species, for respective increases from 4.3% to 6.4% mismatches in the marker gene chvA. This means that there was only a 1.13-fold decrease in recombination frequencies for recombination events at both edges of the species border. Hence, from the findings of this investigation, we conclude that-025EFat least in this taxon-025EFsexual isolation based on homologous recombination is likely not high enough to strongly hamper gene flow between species as compared with gene flow between distantly related members of the same species. The 70% relative binding ratio cutoff used to define bacterial species is likely correlated to only minor declines in homologous recombination frequencies. Consequently, the sequence diversity, as a mechanistic factor for the efficiency of recombination (as assayed in the laboratory), appears to play little role in the genetic cohesion of bacterial species, and thus, the genomic species definition for prokaryotes is definitively not reconcilable with the biological species concept for eukaryotes.