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Genomic panorama of Bradyrhizobium japonicum CPAC 15, a commercial inoculant strain largely established in Brazilian soils and belonging to the same serogroup as USDA 123



Genomic panorama of Bradyrhizobium japonicum CPAC 15, a commercial inoculant strain largely established in Brazilian soils and belonging to the same serogroup as USDA 123



Soil Biology and Biochemistry 40(11): 2743-2753



Of the many genomes of prokaryotes that have been sequenced, most are pathogenic organisms and very few of agriculturally beneficial bacteria. Soybean, the most important cash crop in Brazil, can provide its need for nitrogen through a symbiosis with exotic strains of bradyrhizobia. Bradyrhizobium japonicum strain CPAC 15 (equates to SEMIA 5079, the same serogroup as USDA 123), which is a highly competitive commercial strain applied to soybean crops since the early 1990s, is now established on several millions of hectares. As financial resources for sequencing genomes are still very limited in developing countries, a panoramic genomic view of CPAC 15 was generated. A total of 4328 shotgun reads resulted in 2,046,740 bp with a phred score ≥ 20; the assemblage resulted in 1106 phrap contigs scattered by 69 scaffolds and 966 isolated contigs, with an average of 2.5 reads per contig, covering approximately 13% of the genome. Annotation identified 1371 coding DNA sequences (CDSs), 53% with putative known functions, 23% encoding conserved hypothetical and 24% hypothetical genes, representing about 16% of the estimated putative genes. Several comparisons – on COG and KEGG databases, tRNAs, transposases, G + C content of CPAC 15 with the complete genome of B. japonicum strain USDA 110 indicated a successful coverage of the whole genome. However, the two strains were surprisingly different, as at least 35% of the CDS of CPAC 15 shows higher similarity to microorganisms other than strain USDA 110. Several new putative genes and others with low similarity to USDA 110, were identified. These were related to nodulation, interaction with the host plant and adaptation, e.g., nodB, nodW, ndvA, effector nopP, genes of secretion systems, transporters and environmentally related genes.

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Accession: 022710946

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DOI: 10.1016/j.soilbio.2008.07.016


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