Abstract
Comparative genomic hybridization (CGH) was performed with nine strains of Bradyrhizobium japonicum (a symbiotic nitrogen-fixing bacterium associated with soybean) and eight other members of the Bradyrhizobiaceae by DNA macroarray of B. japonicum USDA110. CGH clearly discriminated genomic variations in B. japonicum strains, but similar CGH patterns were observed in other members of the Bradyrhizobiaceae. The most variable regions were 14 genomic islands (4–97 kb) and low G+C regions on the USDA110 genome, some of which were missing in several strains of B. japonicum and other members of the Bradyrhizobiaceae. The CGH profiles of B. japonicum were classified into three genome types: 110, 122 and 6. Analysis of DNA sequences around the boundary regions showed that at least seven genomic islands were missing in genome type 122 as compared with type 110. Phylogenetic analysis for internal transcribed sequences revealed that strains belonging to genome types 110 and 122 formed separate clades. Thus genomic islands were horizontally inserted into the ancestor genome of type 110 after divergence of the type 110 and 122 strains. To search for functional relationships of variable genomic islands, we conducted linear models of the correlation between the existence of genomic regions and the parameters associated with symbiotic nitrogen fixation in soybean. Variable genomic regions including genomic islands were associated with the enhancement of symbiotic nitrogen fixation in B. japonicum USDA110.
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Acknowledgements
This study was supported in part by a grant-in-aid for Scientific Research on Priority Area ‘Comparative Genomics’, by grants-in-aid for Scientific Research (no. 17380046), by a grant from PROBRAIN, by Special Coordination Funds for Promoting Science and Technology and by a grant from the Tokachi Federation of Agricultural Cooperatives. We thank H Kouchi (National Institute of Agrobiological Sciences), C Harwood (The University of Iowa) and E Giraud (French National Institute for Agricultural Research) for array spotting, provision of R. palustris CGA009 and provision of Bradyrhizobium sp. strains ORS278 and BTAi1, respectively.
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Itakura, M., Saeki, K., Omori, H. et al. Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members. ISME J 3, 326–339 (2009). https://doi.org/10.1038/ismej.2008.88
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DOI: https://doi.org/10.1038/ismej.2008.88
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