Cheng Kun, Rong Xiaoying, Huang Ying
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
Mol Phylogenet Evol. 2016 Sep;102:246-54. doi: 10.1016/j.ympev.2016.06.004. Epub 2016 Jun 18.
Homologous recombination is increasingly being recognized as a driving force in microbial evolution. However, recombination in streptomycetes, a rich source of diverse secondary metabolites, particularly among different species, remains minimally investigated. In this study, the largest sample of Streptomyces species to date, consisting of 142 type strains spanning the genus, with available sequences of 16S rRNA, atpD, gyrB, recA, rpoB and trpB genes, were collected and subjected to a comprehensive population genetic analysis to generate an overall estimate of the level of Streptomyces interspecies genetic exchange and its effect on the evolution of this genus. The results indicate frequent homologous recombination among Streptomyces species, which occurred three times more frequently and was nearly 14 times more important than point mutation in nucleotide sequence divergence (ρ/θw=3.10, r/m=13.74). As a result, a facilitating effect on the evolutionary process and confusion in phylogenetic relationships were observed, as well as a number of specific transfer events of the six gene fragments. A resultant phylogenetic network depicted extensive horizontal genetic exchange which decays clonality in streptomycetes. Moreover, seven evolutionary lineage groups were identified in the present sample in the Structure analysis, generally consistent with morphological and physiological data, and the contribution of recombination was detected to be varied among them. Our analyses demonstrated a reticulate evolution within Streptomyces due to the high level of interspecies gene exchange, which greatly challenges the traditional tree-shaped phylogeny in this genus and may advance our evolutionary understanding of a genuine Streptomyces species.
同源重组日益被认为是微生物进化的驱动力。然而，链霉菌（丰富多样的次级代谢产物来源，尤其是在不同物种之间）中的重组，仍极少被研究。在本研究中，收集了迄今为止最大的链霉菌物种样本，由涵盖该属的142个模式菌株组成，具有16S rRNA、atpD、gyrB、recA、rpoB和trpB基因的可用序列，并对其进行了全面的群体遗传分析，以全面估计链霉菌种间基因交换水平及其对该属进化的影响。结果表明链霉菌物种间频繁发生同源重组，其发生频率比点突变更高3倍，在核苷酸序列差异中其重要性几乎是点突变的14倍（ρ/θw = 3.10，r/m = 13.74）。结果观察到对进化过程有促进作用以及系统发育关系混乱，还有六个基因片段的一些特定转移事件。由此产生的系统发育网络描绘了广泛的水平基因交换，这削弱了链霉菌的克隆性。此外，在结构分析中，在本样本中鉴定出七个进化谱系组，总体上与形态学和生理学数据一致，并且检测到重组在它们之间的贡献有所不同。我们的分析表明，由于种间基因交换水平高，链霉菌内存在网状进化，这极大地挑战了该属传统的树形系统发育，并可能推进我们对真正链霉菌物种的进化理解。
