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Open Access Research article

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

Shanming Wang1, Baohai Hao2, Jiarui Li3, Huilin Gu1, Jieli Peng1, Fuli Xie1, Xinyin Zhao3, Christian Frech3, Nansheng Chen13*, Binguang Ma2* and Youguo Li1*

Author Affiliations

1 State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China

2 Center for Bioinformatics, School of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China

3 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada

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BMC Genomics 2014, 15:440  doi:10.1186/1471-2164-15-440

Published: 6 June 2014

Abstract

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.

Keywords:
Mesorhizobium huakuii 7653R; Genome sequencing; Comparative analysis; Host specificity; Symbiosis island