Qiu Wei-Gang, Schutzer Steven E, Bruno John F, Attie Oliver, Xu Yun, Dunn John J, Fraser Claire M, Casjens Sherwood R, Luft Benjamin J
Department of Biological Sciences, Hunter College of the City University of New York, 695 Park Avenue, New York, NY 10021, USA.
Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14150-5. doi: 10.1073/pnas.0402745101. Epub 2004 Sep 16.
Comparative genomics of closely related bacterial isolates is a powerful method for uncovering virulence and other important genome elements. We determined draft sequences (8-fold coverage) of the genomes of strains JD1 and N40 of Borrelia burgdorferi sensu stricto, the causative agent of Lyme disease, and we compared the predicted genes from the two genomes with those from the previously sequenced B31 genome. The three genomes are closely related and are evolutionarily approximately equidistant ( approximately 0.5% pairwise nucleotide differences on the main chromosome). We used a Poisson model of nucleotide substitution to screen for genes with elevated levels of nucleotide polymorphisms. The three-way genome comparison allowed distinction between polymorphisms introduced by mutations and those introduced by recombination using the method of phylogenetic partitioning. Tests for recombination suggested that patches of high-density nucleotide polymorphisms on the chromosome and plasmids arise by DNA exchange. The role of recombination as the main mechanism driving B. burgdorferi diversification was confirmed by multilocus sequence typing of 18 clinical isolates at 18 polymorphic loci. A strong linkage between the multilocus sequence genotypes and the major alleles of outer-surface protein C (ospC) suggested that balancing selection at ospC is a dominant force maintaining B. burgdorferi diversity in local populations. We conclude that B. burgdorferi undergoes genome-wide genetic exchange, including plasmid transfers, and previous reports of its clonality are artifacts from the use of geographically and ecological isolated samples. Frequent recombination implies a potential for rapid adaptive evolution and a possible polygenic basis of B. burgdorferi pathogenicity.
对密切相关的细菌分离株进行比较基因组学研究是揭示毒力和其他重要基因组元件的有力方法。我们测定了莱姆病病原体狭义伯氏疏螺旋体菌株JD1和N40基因组的草图序列（8倍覆盖），并将这两个基因组预测的基因与之前测序的B31基因组的基因进行了比较。这三个基因组密切相关，在进化上大致等距（主染色体上两两核苷酸差异约为0.5%）。我们使用核苷酸替换的泊松模型筛选核苷酸多态性水平升高的基因。通过系统发育划分方法，三基因组比较能够区分由突变引入的多态性和由重组引入的多态性。重组检测表明，染色体和质粒上高密度核苷酸多态性区域是由DNA交换产生的。对18个临床分离株在18个多态性位点进行多位点序列分型，证实了重组作为驱动伯氏疏螺旋体多样化的主要机制的作用。多位点序列基因型与外表面蛋白C（ospC）主要等位基因之间的强连锁表明，ospC处的平衡选择是维持当地种群中伯氏疏螺旋体多样性的主导力量。我们得出结论，伯氏疏螺旋体经历全基因组遗传交换，包括质粒转移，其之前关于克隆性的报道是使用地理和生态隔离样本产生的假象。频繁的重组意味着快速适应性进化的潜力以及伯氏疏螺旋体致病性可能的多基因基础。
