Comparative Genomics of Major Clonal Groups of a Lyme Disease Pathogen

描述(申请人提供)：莱姆病是美国最流行和传播速度最快的媒介传播传染病。它是由伯氏疏螺旋体细菌引起的，由鹿扁虱传播。至少有15个不同基因的莱姆病病原体克隆群在美国东北部流行，那里每年报告的莱姆病病例超过80%。这些克隆群体在野生动物流行率和人类致病性方面存在差异。2006年，包括PI在内的一个由六名研究人员组成的小组启动了一个由NIH/NIAID资助的为期两年的项目，产生17个伯氏杆菌分离株的全基因组序列，目的是确定克隆变异在环境侵袭性和人类毒力方面的遗传基础。在这里，PI提出了一项研究，通过对12个最常见的克隆群体进行比较基因组分析来完成NIAID全基因组测序项目的目标。 具体目标是：首先，我们将在系统发育框架内识别特定菌株的基因组变化。我们将鉴定和比对主要染色体、同源质粒和同源编码序列。我们将根据染色体DNA序列推断基于基因组的系统发育，以便在这些克隆群进化多样化的过程中，将菌株在基因组内容、基因组组织和DNA序列方面的差异映射到不同的阶段。其次，我们将通过测试自然选择的影响来区分更多的相应(例如，适应性的)基因组变化与较小的(例如，随机的)基因组变化。我们将通过序列保守来识别对基因调控重要的基因间序列，通过相对于同义率的高非同义核苷酸替换率来识别对伯氏杆菌适应至关重要的基因(例如，导致逃避宿主免疫的表面脂蛋白)，通过比较最近分离的姊妹克隆来识别与初始适应性克隆分歧相关的基因。第三，我们将开发和维护一个网站，以促进伯氏杆菌比较基因组信息的公开传播，例如针对高毒力克隆群的基因组变化。目前尚不清楚为什么莱姆病细菌的某些菌株比其他菌株更具致病性。我们将比较高毒力和低毒力菌株的基因组，以确定导致致病性的基因。与毒力相关的基因组元素是设计疗法和疫苗的主要目标。

DESCRIPTION (provided by applicant): Lyme disease is the most prevalent and a fast spreading vector-borne infectious disease in the U.S. It is caused by a spirochetal bacterium Borrelia burgdorferi and transmitted by the deer tick Ixodes scapularis. At least 15 genetically distinct clonal groups of the Lyme disease pathogen are circulating in the northeastern U.S., where over 80% of the Lyme disease cases are reported annually. These clonal groups differ in their wildlife prevalence and human pathogenecity. In 2006, a group of six investigators including the PI have initiated a NIH/NIAID-funded 2-year project producing the whole-genome sequences of 17 B. burgdorferi isolates, with the goal of identifying the genetic basis of clone variations in environmental invasiveness and human virulence. Here, the PI proposes a study to complete the goal of the NIAID whole-genome sequencing project by performing the comparative genome analysis of 12 most common clonal groups. Specific aims are: First, we will identify strain-specific genome changes in a phylogenetic framework. We will identify and align the main chromosomes, orthologous plasmids, and orthologous coding sequences. We will infer a genome-based phylogeny based on chromosomal DNA sequences, so that the strain differences in genome content, genome organization, and DNA sequences can be mapped to different stages during the evolutionary diversification of these clonal groups. Second, we will distinguish more consequential (e.g., adaptive) genomic changes from the lesser (e.g., random) ones by testing for the influence of natural selection. We will identify intergenic sequences important for gene regulation by their sequence conservation, genes critical for B. burgdorferi adaptation (e.g., surface lipoproteins conferring escape from host immunity) by their high non-synonymous nucleotide substitution rates relative to the synonymous rates, genes associated with initial adaptive clonal divergence by comparing the most recently diverged sister clones. Third, we will develop and maintain a website to facilitate the public dissemination of B. burgdorferi comparative genome information, such as genomic changes specific to a high-virulence clonal group. It is unknown why some strains of the Lyme disease bacteria are more pathogenic than others. We will compare the genomes of high- and low-virulence strains to identify the genes contributing to pathogenecity. Virulence-related genome elements are prime targets for designing therapeutics and vaccines.