Zhang Xian, Liu Xueduan, Yang Fei, Chen Lv
Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
Front Microbiol. 2018 Mar 27;9:577. doi: 10.3389/fmicb.2018.00577. eCollection 2018.
Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within species at the genome level. Mathematical models were further constructed to extrapolate the expansion of genomes (an 'open' pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the genomes. In short, our genome-wide analyses bridge the relation between genetic variation of with its evolutionary adaptation.
生态位适应长期以来被认为会驱动物种内部分化和物种形成，然而，关于其与微生物基因组遗传变异的相关性的知识相对有限。以某物种为例，我们对五个已识别菌株的基因组特征进行了详细分析。基因组到基因组距离计算初步确定了空间距离和环境异质性在基因组水平上对该物种内物种变异可能产生的作用。进一步构建数学模型来推断该物种基因组（一个“开放”的泛基因组）的扩展情况，这表明随着新测序基因组的出现会有新基因产生。对多种移动遗传元件（如转座酶、整合酶和噬菌体相关基因）的鉴定揭示了水平基因转移事件的普遍性，这是一种重要的进化机制，为新功能的获得以及微生物基因组的遗传分化提供了途径。综合分析还表明，广义上因基因丢失导致的基因组缩减可能促成了所观察到的多样性。因此，我们推断出一个合理的解释来应对这一观察结果：群落依赖性适应可能会节约整个群落有限的资源。鉴于新基因的引入伴随着其他一些基因的同时舍弃，我们的结果提供了关于该物种基因组内环境适应的生物学适应性代价的简要情况。简而言之，我们的全基因组分析揭示了该物种遗传变异与其进化适应之间的关系。
