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Bradyrhizobium elkanii  USDA 76 T  (INSCD = ARAG), the type strain for  Bradyrhizobium elkanii , is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of  Glycine max  (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume,  B. elkanii  USDA 76 T  was selected as part of the DOE Joint Genome Institute 2010  Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria  sequencing project. Here the symbiotic abilities of  B. elkanii  USDA 76 T  are described, together with its genome sequence information and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2 scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only encoding genes. The  B. elkanii  USDA 76 T  genome contains a low GC content region with symbiotic  nod  and  fix  genes, indicating the presence of a symbiotic island integration. A comparison of five  B. elkanii  genomes that formed a clique revealed that 356 of the 9060 protein coding genes of USDA 76 T  were unique, including 22 genes of an intact resident prophage. A conserved set of 7556 genes were also identified for this species, including genes encoding a general secretion pathway as well as type II, III, IV and VI secretion system proteins. The type III secretion system has previously been characterized as a host determinant for  Rj  and/or  rj  soybean cultivars. Here we show that the USDA 76 T  genome contains genes encoding all the type III secretion system components, including a translocon complex protein NopX required for the introduction of effector proteins into host cells. While many bradyrhizobial strains are unable to nodulate the soybean cultivar Clark ( rj1 ), USDA 76 T  was able to elicit nodules on Clark ( rj1 ), although in reduced numbers, when plants were grown in Leonard jars containing sand or vermiculite. In these conditions, we postulate that the presence of NopX allows USDA 76 T  to introduce various effector molecules into this host to enable nodulation.   Electronic supplementary material  The online version of this article (doi:10.1186/s40793-017-0238-2) contains supplementary material, which is available to authorized users.

High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr