分类学研究不但要求符合其重要的生物表型与"生态境"，还要求符合其进化演变历程，与生物的系统发育关系保持一致。在基因组测序技术高度发展的今天，能充分利用基因组信息，还原基因组的进化历程，以此为基础构建生物系统发育关系就成为分类学研究的关键。目前基于基因组信息的系统发育分析主要利用各种序列特征，如gene、蛋白、domain来构建系统发育树，但这些序列特征只能反应部分进化信息，常导致系统发育树错误，造成分类学研究困扰。本项目提出一种新的序列特征，同源子序列，初步研究表明它能作为基因间的交换片段来反映基因组的各种进化事件。本研究拟通过"同源子序列"来挖掘基因进化事件，估计基因复制、融合、裂解、重组等对基因组进化的影响，还原基因组进化历程，并据此构建基于同源子序列的系统发育学方法，阐述某些进化关系存在争议的菌株间的系统发育关系，为原核生物的分类提供一个新的视角与方法。

Taxonomic studies must not only aim at the important biological phenotypes and niches of organisms, but also conform to the course of evolution to be consistent with the phylogeny. In today's rapid development of genome sequencing technology, the phylogenetic tree constructed with full of genome information to restore the process of genome evolution becomes the key of taxonomic studies. At present, the genome-scale phylogenetic analysis uses various sequence features, like gene, protein and domain, to construct phylogenetic trees. However, the features reflect only part of the evolutionary information. As a result, some errors occur in phylogenetic tree, troubling the taxonomic research. This project provides a newly defined sequence feature-homologous subsequence. Homologous subsequence could act as the exchange segment between genes to reflect the various events of genome evolution. This research intends to dig into the events of gene evolution based on homologous subsequence, and then estimates the effect of gene duplication, fusion, fission and recombination on genome evolution; and accordingly constructs a new phylogenetic method based on homologous subsequence to elaborate the phylogenetic relationship of strains with dispute in evolution, providing a new perspective and method for the taxonomy of prokaryote.