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Background  Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between  Mesorhizobium  strain MAFF303099 and  M. huakuii . To define underlying causes for the rather striking difference in host specificity between  M. huakuii  strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of  Mesorhizobium  to form genomic islands would enrich our knowledge of how genome dynamics may contribute to  Mesorhizobium  evolution in general.    Results  In this study, we sequenced the complete genome of 7653R and compared it with five other  Mesorhizobium  genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral  Mesorhizobium  genomic island that has evolved into diverse forms in different  Mesorhizobium  species.    Conclusions  Our ortholog and synteny analyses firmly establish MAFF303099 as a strain of  M. huakuii . Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome.    Electronic supplementary material  The online version of this article (doi: 10.1186/1471-2164-15-440) contains supplementary material, which is available to authorized users.

Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics