Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analysed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

中文翻译：

---

与共生固氮相关的质粒不仅在功能上协同作用，而且可能在根瘤菌科中进化了一段时间。

根瘤菌是能够形成与豆科植物相关的共生固氮根瘤的土壤细菌。在快速增长的豆科植物结瘤的根瘤菌，如在家庭中的物种根瘤菌科，共生质粒是用于固氮共生的主要遗传基础，并且易受水平基因转移。进一步了解根瘤菌科的共生进化，我们基于 92 个类型/参考菌株的基因组分析了该家族的泛基因组，并使用系统基因组学方法重建了其系统发育。有趣的是，尽管发生在染色体区域的遗传扩展是泛基因组中低频灵活基因家族比例高的主要原因，但与辅助质粒相关的基因增益事件将更多基因引入固氮物种的基因组. 对于共生质粒，虽然经常发生水平基因转移，但转移可能会受到例如宿主的物理隔离和土壤条件的阻碍，即使在系统发育相近的物种之间也是如此。在与豆科宿主共同进化的过程中，质粒系统，包括附属质粒和共生质粒，可能已经进化了一段时间，并为根瘤菌提供了适应各种环境条件的能力，并帮助它们实现了固氮。这些发现提供了对系统发育的新见解根瘤菌科，促进我们对共生固氮进化的理解。