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

Abstract

BackgroundEvidence 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.ResultsIn 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.ConclusionsOur 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 materialThe online version of this article (doi: 10.1186/1471-2164-15-440) contains supplementary material, which is available to authorized users.

Genetic and Genomic Diversity Studies of Acacia Symbionts in Senegal Reveal New Species of Mesorhizobium with a Putative Geographical Pattern

“…The use of ANI seems to be a good species assessment in the Mesorhizobium genus, as there was also no conflict of ANI values between known Mesorhizobium species ( Table 4 , all known species comparison gave ANI <95%). The ANI between reference strains also confirms the belonging of the strain MAFF303099 to a separate species from M. loti (89.35% ANI with M. loti USDA3471 T ) as suggested by Turner et al [ 65 ] and Wang et al [ 66 ]. Our study also confirms the good performance of the 5 markers used ( atp D, dna J, gyr B, rec A and gln A) in Mesorhizobium diversity studies as previously reported for rhizobia [ 28 , 35 – 37 , 39 , 53 , 67 ].…”

“… §: NCBI taxon number at http://www.ncbi.nlm.nih.gov/taxonomy . %: Strain MAFF303099 was assigned to the M. huakuii species in previous reports [ 65 , 66 ]. AN: Accession Number.…”

Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island

“…A. caulinodans was isolated from stem nodules and is thought to be epiphytic bacteria (40), whereas S. rostrata sinorhizobia were isolated from root nodules and are abundant in the soil and in the rhizosphere (41). Transfer of the ICE Ac into another rhizobium results in the coexistence of different symbiotic modules on two different replicons of the same strain, a situation already observed in natura (11). ICE Ac transfer allows the recipient rhizobial genome to diversify its range of symbiotic hosts and form nitrogen-fixing nodules on S. rostrata, in addition to its natural symbiotic partner.…”

Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools

“…The acidification may lead to the segregation of unknown effector molecules and create changes in the host cell endosome that generate a new intracellular compartment in which the attacker can replicate [28]. The secretion systems of types III, IV and VI and the nodulation factors are considered responsible for lead host specificity in Mesorhizobium huakuii [4]. …”

“…The growth rate of Mesorhizobium is intermediate between the genera Rhizobium and Bradyrhizobium and is one of the largest genera. Additionally, the Mesorhizobium genera consists of 24 species found in Asia, Europe, the Mediterranean region and Africa [4, 5]. …”