Genetic Divergence of Bradyrhizobium Strains Nodulating Soybeans as Revealed by Multilocus Sequence Analysis of Genes Inside and Outside the Symbiosis Island

Abstract

ABSTRACTThe genusBradyrhizobiumhas been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels amongBradyrhizobiumstrains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019,thrA, andtruA). This was also supported by analyses of eight genes outside the symbiosis island (“off-island” genes;SMc00019,thrA,truA,fabB,glyA,phyR,exoN, andhsfA). However, seven genes inside the symbiosis island (“island” genes;nifA,nifH,nodC,nodV,fixA,trpD, andrhcC2) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored byBradyrhizobium japonicum,Bradyrhizobium diazoefficiens,Bradyrhizobium huanghuaihaiense,Bradyrhizobium liaoningense,Bradyrhizobium daqingense,Bradyrhizobiumsp. I,Bradyrhizobiumsp. III, andBradyrhizobiumsp. IV) was not found inBradyrhizobium yuanmingense,Bradyrhizobiumsp. II, orBradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes.