title: Genetic divergence of bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island.
abstract: The genus Bradyrhizobium has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among Bradyrhizobium strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019, thrA, and truA). This was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA). However, seven genes inside the symbiosis island ("island" genes; nifA, nifH, nodC, nodV, fixA, trpD, and rhcC2) 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 by Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, Bradyrhizobium huanghuaihaiense, Bradyrhizobium liaoningense, Bradyrhizobium daqingense, Bradyrhizobium sp. I, Bradyrhizobium sp. III, and Bradyrhizobium sp. IV) was not found in Bradyrhizobium yuanmingense, Bradyrhizobium sp. II, or Bradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes.
authors.affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
authors.forename: Xing Xing
authors.initials: XX
authors.lastname: Zhang
authors.forename: Hui Juan
authors.initials: HJ
authors.lastname: Guo
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.forename: Xin Hua
authors.initials: XH
authors.lastname: Sui
authors.forename: Yan Ming
authors.initials: YM
authors.lastname: Zhang
authors.forename: En Tao
authors.initials: ET
authors.lastname: Wang
authors.forename: Chang Fu
authors.initials: CF
authors.lastname: Tian
authors.forename: Wen Xin
authors.initials: WX
authors.lastname: Chen
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D020369:Bradyrhizobium / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D014644:Genetic Variation; D044404:Genomic Islands; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D055170:Plant Root Nodulation; D053204:Root Nodules, Plant / Q000382:microbiology*; D013025:Glycine max / Q000382:microbiology* / Q000502:physiology; D013559:Symbiosis
chemical_list: D001426:Bacterial Proteins