Whole-genome Sequencing And Comparative Genomic Analysis Of Mesorhizobium Huakuii Strain7653R

In this thesis, we sequenced, assembled, and annotated the whole genome sequence of Mesorhizobium huakuii strain7653R, and performed comparative analysis with five strains (Mesorhizobium huakuii bv. loti MAFF303099, Mesorhizobium loti R7A, Mesorhizobium ciceri bv. biserrulae WSM1271, Mesorhizobium australicum WSM2073, and Mesorhizobium opportunistum WSM2075) from different species in Mesorhizobium. It reveals the similarities and differences between them in genome characteristics, genome alignment, orthologs, nodulation and nitrogen fixation genes, surface polysaccharides, secretion system, and so on. We try to resolve some scientific problems, such as phylogenetic position of rhizobia, host specificity, symbiosis island dynamics, origin and evolution of plasmids, and so on.Are there differences between the six Mesorhizobium strains in genome features? How is the linear relationship between six genomes? And how much difference between them in biological functions. Genome comparisons between them are required to answer all these questions. The phylogenetic position of strain MAFF303099has been in controversy. Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099and M. huakuii. Although MAFF303099belongs to M. huakuii, it is distinctly different from M. huakuii strain7653R in host specificity. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain7653R and MAFF303099, several probable determinants also require comparison at the genomic level. These probable determinants mainly include nodulation factor, surface polysaccharides, and secreted proteins. 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. Symbiosis plasmids of7653R share the same genome features with genomic islands from other five strains. Then, is there any relationship among them? It depends on the studies on dynamics of genomic island.In this study, we described and submitted the complete genome sequence of7653R (GenBank accession number:CP006581-CP006583), and compared it with five other Mesorhizobium genomes. Our6,881,675-bp assembly of the M. huakuii7653R genome consisted of three circular replicons of6,364,365bp (chromosome),193,835bp (plasmid pMhu7653Ra), and323,475bp (plasmid pMhu7653Rb). Genomes of7653R and MAFF303099were 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. These differences mainly focus on two aspects: biosynthesis pathway of nodulation factor and modifications, several types of secretion systems. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species, and analysed the possibility of7653R symbiosis plasmids originating from ancestral genomic island.Above-mentioned genome comparison results indicate that:(1) Our ortholog and synteny analyses firmly establish MAFF303099as a strain of M. huakuii.(2) Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of7653R and MAFF303099strains.(3) For Mesorhizobium strains, similar specific site of chromosome has a genomic island. The plasmids of7653R may have arisen by excision of the original genomic island from the7653R chromosome.