The symbiosis between legumes and nodulating Proteobacteria (so-called rhizobia) contributes greatly to nitrogen fixation in terrestrial ecosystems. Root nodulating Proteobacteria produce nodulation (Nod) factors during the initiation of rhizobial nodule organogenesis on the roots of legumes. Here, we screened the Nod factor production capacity of the previously reported nodule inducing Proteobacteria genera using their genome sequences and assessed the evolutionary history of symbiosis based on phylogenomics. Our analysis revealed 12 genera as potentially Nod factor producing taxa exclusively from alpha- and beta-Proteobacteria. Based on molecular clock analysis, we estimate that rhizobial nitrogen-fixing symbiosis appeared for the first time about 51 Mya (Eocene epoch) in Rhizobiaceae, and it was laterally transferred to multiple symbiotic taxa in alpha- and beta-Proteobacteria. Coevolutionary tests conducted for measuring the phylogenetic congruence between hosts and symbionts revealed only weak topological similarity between legumes and their bacterial symbionts. We conclude that frequent lateral transfer of symbiotic genes, facultative symbiotic nature of rhizobia, differential evolutionary processes of chromosome versus plasmids, and complex multispecies coevolutionary processes have shaped the rhizobia-host associations.

豆科植物和结瘤变形菌（所谓的根瘤菌）之间的共生对陆地生态系统的固氮作用有很大贡献。根结瘤变形菌在豆类根部的根瘤菌根瘤器官发生过程中产生结瘤 (Nod) 因子。在这里，我们使用基因组序列筛选了先前报道的结节诱导变形菌属的 Nod 因子生产能力，并基于系统基因组学评估了共生的进化历史。我们的分析揭示了 12 个属是潜在的 Nod 因子，它们完全来自 α- 和 β-变形菌。根据分子钟分析，我们估计根瘤菌固氮共生首次出现在根瘤菌科约51 Mya（始新世时期），并且它被横向转移到α-和β-变形菌中的多个共生分类群中。为测量宿主和共生体之间的系统发育一致性而进行的共同进化测试表明，豆科植物与其细菌共生体之间只有微弱的拓扑相似性。我们得出结论，共生基因的频繁横向转移，根瘤菌的兼性共生性质，染色体的差异进化过程与质粒相比，复杂的多物种协同进化过程塑造了根瘤菌-宿主的关联。