极端微生物宏基因组微进化的计算生物学研究

To clarify several essential issues of microevolution process and mechanisms of the extremophiles, the project aims to develop the novel computational methods and tools, and apply them to the metagenomics studies. To specify, we will focus on the microbial community under the extreme environment, currently accompanied by a large of high-throughput sequecing metagenomic data, and devote to the microevolution of extremophile metagenomes by a series of computatinal methods and tools. We plan to first predict and locate all key genes associated with the extreme enviromentent, and then present their functionary annotation based on several evidences. Then, we will carry out a comparative genomics analysis about the key genes and other genes for a genome or among the colsely-related genomes in the microbial comunity, which are for both the coding regions and their regulatory regions of transcription and translation etc. The project further applies a series methods and tools, to compare the genomic structure for decribing changes of these key genes and thier regulation ways; to compare the functionary classification distribution for describing the key role of key genes in the community; to comprehensively analyze the metabolic pathways of the microbial community and the individual bacterial or archaeal genome, leading to the further understanding of the social behaviour of the microbial community and the social relations among the species in the community. The studies will devote to the understanding of the molecular mechanism of the extremephiles to adapt the enviroments.

致力于发展新的计算生物学方法并运用于宏基因组分析，阐明极端微生物微进化过程和机制的若干关键问题。主要研究内容为：以极端环境下的微生物群落为研究对象，基于当前高通量测序技术获得的宏基因组数据，围绕极端微生物基因组微进化的主题，发展和运用一系列的计算生物学新方法和新技术，首先预测、定位与极端环境相关的关键基因；在此基础上进行关键基因的功能注释，并定量刻画近缘物种之间及同一物种内的关键基因及其转录、翻译等调控机制的演化；进一步通过基因组比较、功能分类分析、代谢网络分析等手段，分析不同物种及其关键基因适应和影响极端环境的分子机制。课题的立项属于围绕本计划第二个重点支持方向的计算生物学新方法研究，并提出了明确的技术路线和解决方案。

本项目的研究计划为：以极端环境下的微生物群落为研究对象，基于当前高通量测序技术获得的宏基因组数据，围绕极端微生物基因组微进化的主题，发展和运用一系列的计算生物学新方法和新技术，首先预测、定位与极端环境相关的关键基因；在此基础上进行关键基因的功能注释，并定量刻画近缘物种之间及同一物种内的关键基因及其转录、翻译等调控机制的演化；进一步通过基因组比较、功能分类分析、代谢网络分析等手段，分析不同物种及其关键基因适应和影响极端环境的分子机制。总体来说，本项目的执行严格按照计划进行。已发表SCI论文7篇，正在审稿或待投稿论文3篇。研究结果的可能贡献为：（1）建立了极端环境微生物群落的种群动力学模型，对探讨多基因作用下的微进化具有一定的启发意义和应用前景，可能籍此提出一种基于基因功能和极端环境下的环境因子的物种进化模型；（2）研究了极端环境下微生物微进化过程中的重要途径——HGT事件、基因功能对极端环境的适应性，对微进化的理解具有一定的意义；（3）发展了一系列的计算生物学方法。