原核生物物种界定长时间备受争议主要是因为对微进化的基本单位-种群的研究和认识不足。重组在原核生物中广泛存在，主要以同源重组和基因横向转移(HGT)两种方式分别存在于近缘个体间和远缘个体间。链霉菌(streptomycetes)是一类有着简单形态分化的丝状细菌，以产生抗生素而著称，具有高度的遗传、功能和生态多样性。本项目以我们构建的链霉菌多位点序列分析(MLSA)平台为基础，选择代表性的链霉菌种群；运用群体遗传学和系统学手段，通过分析比较不同种群的同源重组率、突变率和遗传结构，解析链霉菌不同物种的群体结构；运用基因组学及生物信息学方法，通过分析比较种内不同亚群间和近缘种间的基因组序列，研究同源重组和HGT的频率和范围，揭示同源重组和HGT对链霉菌生态分化和基因组变异的作用。研究结果将阐明重组是否为链霉菌物种形成和维持的内在主动力及其对多样性的贡献，推动链霉菌微进化理论和物种概念的进一步发展。

The lack of investigation and understanding on bacterial and archaeal populations has resulted in heated debates on prokaryotic species. Furthermore, the newly appreciated widespread recombination in the microbial world, either in the form of homologous recombination between close relatives or horizontal gene transfer (HGT) between distantly related strains, has challenged our concepts of evolution. Streptomycetes are a complex group of filamentous bacteria, which are ubiquitous in nature, well known producers of antibiotics and bioactive compounds, and exhibit high levels of genetic, functional and ecological diversities. In this study, we will choose several representative Streptomyces species populations on the basis of the multilocus sequence analysis (MLSA) scheme we previously established for streptomycetes. We will dissect the population structures of different species, by means of population genetics and systematics, and by analysis and comparison of the homologous recombination rate, mutation rate and genetic structure. We will also quantify the frequency and range of homologous recombination and HGT among streptomycetes, using genomics and bioinformatics methods, and by analysis and comparison of genomic sequences between intraspecific populations and between closely related species, to uncover the effects of homologous recombination and HGT on ecological differentiation and genome variation among populations. The results of this study are expected to clarify whether recombination is the dominant inner force to shape and sustain Streptomyces species, and its contribution to the streptomycete diversity.