Department of Molecular Evolution, Biomedical Centre, Uppsala University, SE-751 24, Uppsala, Sweden.
BMC Evol Biol. 2012 May 11;12:65. doi: 10.1186/1471-2148-12-65.
Rates of recombination vary by three orders of magnitude in bacteria but the reasons for this variation is unclear. We performed a genome-wide study of recombination rate variation among genes in the intracellular bacterium Bartonella henselae, which has among the lowest estimated ratio of recombination relative to mutation in prokaryotes.
The 1.9 Mb genomes of B. henselae strains IC11, UGA10 and Houston-1 genomes showed only minor gene content variation. Nucleotide sequence divergence levels were less than 1% and the relative rate of recombination to mutation was estimated to 1.1 for the genome overall. Four to eight segments per genome presented significantly enhanced divergences, the most pronounced of which were the virB and trw gene clusters for type IV secretion systems that play essential roles in the infection process. Consistently, multiple recombination events were identified inside these gene clusters. High recombination frequencies were also observed for a gene putatively involved in iron metabolism. A phylogenetic study of this gene in 80 strains of Bartonella quintana, B. henselae and B. grahamii indicated different population structures for each species and revealed horizontal gene transfers across Bartonella species with different host preferences.
Our analysis has shown little novel gene acquisition in B. henselae, indicative of a closed pan-genome, but higher recombination frequencies within the population than previously estimated. We propose that the dramatically increased fixation rate for recombination events at gene clusters for type IV secretion systems is driven by selection for sequence variability.
细菌中的重组率差异可达三个数量级，但这种差异的原因尚不清楚。我们对细胞内细菌巴尔通体亨氏亚种（Bartonella henselae）基因中的重组率变化进行了全基因组研究，该细菌的重组与突变比估计在原核生物中是最低的。
B. henselae 菌株 IC11、UGA10 和休斯顿-1 的 1.9Mb 基因组显示出微小的基因含量差异。核苷酸序列差异水平小于 1%，全基因组的重组与突变相对速率估计为 1.1。每个基因组有 4 到 8 个片段呈现出显著增强的分歧，其中最明显的是 IV 型分泌系统的 virB 和 trw 基因簇，这些基因簇在感染过程中起着至关重要的作用。一致地，在这些基因簇内部鉴定出了多个重组事件。一个推测与铁代谢有关的基因也观察到了高频的重组。对 80 株巴尔通体 quintana、B. henselae 和 B. grahamii 的该基因进行的系统发育研究表明，每个物种的种群结构都不同，并揭示了具有不同宿主偏好的巴尔通体物种之间的水平基因转移。
我们的分析表明，B. henselae 中几乎没有新的基因获得，表明其基因组是封闭的，但与之前估计相比，其种群内的重组频率更高。我们提出，IV 型分泌系统基因簇中重组事件的固定率急剧增加是由对序列变异性的选择驱动的。
