The draft sequence of the genome of Bradyrhizobium elkanii 587 is presented. This was obtained using Illumina Next-Gen DNA sequencing combined with Sanger sequencing. Genes for the pathways involved in biological nitrogen fixation (the nif gene cluster), nod genes including nodABC, and genes for the type III protein secretion system (T3SS) are present.
Bradyrhizobium elkanii 587 is a nitrogen-fixing bacterium that nodulates soybean and is used in commercial inoculants in Brazil (7).The draft genome sequence of B. elkanii 587 was obtained using a combination of Illumina and Sanger reads. A total of 6,020,858 endpaired reads were de novo assembled using Velvet (11) with an average read depth of 28-fold; 42,785 Sanger reads were added to the assembly, resulting in 260 scaffolds (N 50 , 54,941 bp). Scaffold ordering was carried out using Bradyrhizobium japonicum USDA110 as a reference. B. elkanii 587 contains one circular chromosome of 8.8 Mbp with a GϩC content of 62.9%, and no plasmid was detected. Annotation of 9,250 potential open reading frames (ORFs) and 71 tRNA genes was performed using the RAST program (1). Genes of interest were curated and analyzed manually. A single rRNA operon was found, as in B. japonicum USDA110 (4).Genes for the same metabolic pathways found in B. japonicum were found in the genome of B. elkanii 587. Genes encoding the Entner-Doudoroff and Embden-Meyerhof-Parnas pathways for carbohydrate degradation are present.The nif genes nifDKENX-(orf1 to orf7)- fixBCX are present in one cluster. The genes related to nodulation are organized in two regions. The first contains 19 genes, nodUIJ, nopM, nodZ, fixR, nifA, nopM, fixAKLNOGHI, noeE, and nodQP, and includes the nif transcriptional activator (the nifA gene). The second cluster contains five genes, nodD1 and nodABCS. The genes nodT, nopB, nodU, nolY, nolL, and nolV were identified outside the clusters.
