Université de Lorraine, INRA, DynAMic, Nancy, France.
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, France.
mBio. 2019 Sep 3;10(5):e01533-19. doi: 10.1128/mBio.01533-19.
In this work, by comparing genomes of closely related individuals of isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in populations. Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.
在这项工作中，我们通过比较在空间微尺度（毫米或厘米）上分离的密切相关个体的基因组，研究了水平基因转移在自然种群多样化中的程度和影响。我们表明，尽管这些同物种的菌株共享一个最近的共同祖先，但它们都拥有明显不同的基因含量，这意味着大量和快速的基因流动。菌株的附加基因组分布在插入/缺失事件（indels）中，范围从一个到几百个基因。indels 优先位于线性染色体的臂上（约 12Mb），并且似乎形成了重组热点。其中一些含有生物合成基因簇（BGCs），其产物赋予抑制能力，并可能构成公共物品，有利于细菌种群的凝聚力。此外，这些可变性基因中有相当一部分是质粒携带的，或者带有放线菌整合和共轭元件（AICEs）的特征。我们提出，结合是 indel 通量和种群多样性的主要驱动因素。水平基因转移是使细菌基因库多样化的快速有效的方法。目前，关于自然土壤种群中这种基因流动的了解甚少。通过对属于同一物种且在微尺度上分离的菌株进行比较基因组学研究，我们揭示了相当一部分泛基因组经常发生转移。我们表明，它发生在一个时间尺度上，使种群能够多样化，并应对其不断变化的环境，特别是通过生产公共物品。
