湖区日本血吸虫适应山区新环境的分子进化机制

Adaptation to the new environment plays vital role in the transmission and prevalence of parasites. Schistosoma japonicum has a complicated lifecycle. The transmission, epidemic, adaptation and evolution of S. japonicum depend on the environments of habitat, which includes their intermediate host (e.g. snail) and definitive host (e.g. mammalians). By using varied genetic markers, the S. japonicum in China could be divided into two clades: Mountain region (MR) and Lake region along the middle and low reaches of Yangtze River (LR); moreover, their snails are belonged to two different taxa respectively, and the S. japonicum from LR are hard to infect the intermediate host in MR. Applying the whole mitochondrial genome sequences, we investigated the population structure of S. japonicum population from 13 different endemic areas. The results of most recent common ancestor analysis showed that the S. japonicum in MR were migrated from LR, and the differentiation time is almost consistent with the starting of agriculture expansion in China. Furthermore, we also screened the candidates of detected some candidate genes, which show the significant genetic differentiations of S. japonicum between MR and LR base on the partial genome sequences. The hypothesis of this proposal is: with the agriculture expansion, S. japonicum were migrated from LR to MR (i.e. with their definitive host), and this migration forced the rapid evolution of S. japonicum to adapt to the new environment (e.g. to infect the new intermediate snail efficiently). In this proposal, we will re-sequence the whole genome of S. japonicum populations from MR and LR, and then compare their genomics, in order to detect significant differentiated loci / genes and positive selective genes. Furthermore, we will identify the key functional genes, which may help the parasites to adapt to the new environment, in laboratory. This study will hence our understanding of the role of functional genes in the changing environments and, more generally, in adaptive evolution.

适应新环境是寄生虫传播和流行的必要条件。血吸虫具复杂生活史，其传播和流行依赖于对中间宿主钉螺、哺乳动物终宿主和生存环境的适应。我国日本血吸虫流行类型分为湖沼型和山丘型, 湖区和山区钉螺分属不同亚种，且湖区血吸虫难以感染山区钉螺。前期对13个地区日本血吸虫线粒体全基因组分析显示，山区血吸虫是由湖区血吸虫迁徙分化而来，分化时间与稻作农业扩张时间基本吻合；全基因组序列初步比较也发现了候选强烈分化基因位点。科学假设：近万年来,随着稻作文明的扩张，日本血吸虫跟随其终宿主(人\牛等)从长江中下游湖区向西南山区迁徙，迫使日本血吸虫快速进化以迅速适应新环境而传播和流行。本研究将基于我们前期已有日本血吸虫组学数据，对分布于湖区和山区的不同地域株的血吸虫进行全基因组补充测序，通过比较基因组和进化选择分析，发现强烈分化和受选择基因位点，鉴定日本血吸虫适应新环境的关键基因，阐明其适应性进化的分子机制。

血吸虫是一种重要的人兽共患寄生虫，其对环境的适应性进化对血吸虫病的流行传播有重要意义。但其在流行传播过程中适应新环境而产生的遗传变异与其适应性表型的关系还并不清楚。.本研究通过二代测序技术完成了5个流行区13个种群的日本血吸虫线粒体全基因组测序及全基因组重测序，从线粒体基因组层面研究了日本血吸虫物种系统分化历史，并从基因组的层面对湖区日本血吸虫向山区扩散过程中适应性遗传变异特征进行分析，挖掘出一批受到强正向选择的候选基因。主要的研究成果包括：1. 对不同地理来源的日本血吸虫线粒体基因组进行系统进化分析，首次明晰了不同流行区日本血吸虫之间的种系发生关系和分化时间，发现山区血吸虫是由湖区血吸虫分化而来，分化时间大约距今5000年前，并挖掘出区分不同流行区的血吸虫的遗传标记；2. 本研究利用重测序数据对山区和湖区日本血吸虫进行遗传差异分析，获得了山区和湖区血吸虫的SNP位点325,520个，其中同义突变为9,059，非同义突变为7,494；3. 通过对山区和湖区SNP位点进行系统发育、主成分分析及种群结构分析，表明在不同的环境选择压下，山区血吸虫与湖区血吸虫产生了明显的遗传分化；4. 通过FST和Tajima’s D进行多重检验，最终筛选出269个正向选择基因，对这些基因进行了功能富集，发现主要富集在细胞分裂、定殖、囊泡运输、睡眠及内肽酶活性等方面；5. 进一步对受正选择的基因统计dN/dS, 筛选出日本血吸虫中受强正向选择的基因86个，对其中与生长相关的神经调制蛋白GAP-43及免疫球蛋白样因子的蛋白结构进行预测，发现其中关键位点发生变异，可能导致其功能的改变；5. 为改善日本血吸虫基因组质量，我们结合三代测序和二代技术对日本血吸虫基因组进行重测序以及从头拼接，获得了1840个scaffold，N50为1.05M，大大提高了基因组质量，为后续深入分析适应性进化分子机制提供数据基础。本课题通过对山区和湖区的日本血吸虫种群的遗传差异分析，解析了湖区血吸虫适应山区新环境的遗传基础，为进一步解析其适应性进化机制奠定了基础。共发表SCI论文9篇，申请专利两项。