Population Genetic Analysis of Streptomyces albidoflavus Reveals Habitat Barriers to Homologous Recombination in the Diversification of Streptomycetes
Population Genetic Analysis of Streptomyces albidoflavus Reveals Habitat Barriers to Homologous Recombination in the Diversification of Streptomycetes
复制标题
白黄链霉菌的群体遗传分析揭示了链霉菌多样化中同源重组的栖息地障碍
DOI：
10.1128/aem.02925-14
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发表时间：
2015-02-01
影响因子：
4.4
通讯作者：
Huang, Ying
中科院分区：
文献类型：
--
作者：
Cheng, Kun;Rong, Xiaoying;Huang, Ying
摘要研究微生物种群结构以及重组和生态对微生物种群的影响，对于理解微生物的进化和物种形成具有重要意义。链霉菌是一类广泛分布于自然界的细菌，含有丰富的生物活性物质，但很少进行种群遗传学研究。在这项研究中，我们应用了基于五个基因的多位点序列分析(MLSA)方案，对来自不同来源的41株白化链霉菌进行了分析，这些来源主要是昆虫、海洋和土壤。从两两同源性指数(Φw)检验、系统发育不一致性检验、Shimodaira-Hasegawa(SH)检验和网络分析中检测到频繁的重组，这支持了同源重组在链霉菌中的优势。在系统发育和结构2.3.3分析中也观察到了强烈的栖息地信号，表明生态差异在形成种群结构中的重要性。此外，所有三个与栖息地相关的群体，特别是昆虫群体，都显示出彼此之间的基因流动水平显著降低，通常揭示了栖息地重组的障碍。因此，可以推断出同源重组和生态学的综合效应，其中动态进化至少部分平衡于不同生境之间菌株的差异分布限制遗传交流的程度。我们的研究强调了生态学在微生物物种形成中的重要性，揭示了链霉菌进化过程中同源重组和生态分化并存的现象。
ABSTRACT Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φ w ) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes.