Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with in Natural Environments.

To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with , we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that in natural environments was associated with diverse lineages of spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the genes required for symbiosis with behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in -associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of .