Abstract
The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.
Highlights
The process of symbiotic nitrogen fixation is of both agricultural and ecological significance
Lower intensities were detected in the regions corresponding to all 14 small genomic islands identified on the USDA110 genome, which is a common feature of other members of genomes belonging to the USDA6 group
In order to assess the genome size of USDA6T and to confirm its divergence from USDA110 before sequencing, the composition of fragments of genomic DNA digested with two restriction endonucleases, PmeI and SwaI, was analyzed using pulsed-field gel electrophoresis (PFGE)
Summary
The process of symbiotic nitrogen fixation is of both agricultural and ecological significance. It is remarkable that symbiosis islands have only been identified in some rhizobial strains, because, in general, fast-growing rhizobia have the symbiotic plasmid as a cassette for symbiotic nitrogen fixation genes [7]. Lower intensities were detected in the regions corresponding to all 14 small genomic islands identified on the USDA110 genome, which is a common feature of other members of genomes belonging to the USDA6 group This observation indicates that the insertions of genomic islands cause obvious variation between USDA110 and the diverse genomes categorized in the USDA6 group. Phylogenetic analyses based on internal transcribed spacer region of ribosomal DNA (ITS) sequence data have shown that USDA6T belongs to a clade distant from that of USDA110 [15]. In order to investigate the genomic features of the type strain of B. japonicum and conduct detailed comparative analysis between the two B. japonicum strains, we carried out genome sequencing of USDA6T, and compared the genomic features between USDA6T and USDA110
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