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

Authors: REEVE, WAYNE - Murdoch University; VAN BERKUM, PETER - Retired ARS Employee; ARDLEY, JULIE - Murdoch University; TIAN, RUI - Murdoch University; GOLLAGHER, MARGARET - Curtin University; MARINOVA, DORA - Curtin University; Elia, Patrick; REDDY, TBK - Department Of Energy Joint Genome; PILLAY, MANOJ - University Of California; VARGHESE, NEHA - Department Of Energy Joint Genome; SESHADRI, REKHA - Department Of Energy Joint Genome; IVANOVA, NATALIA - Department Of Energy Joint Genome; WOYKE, TANJA - Department Of Energy Joint Genome; BAESHEN, MOHAMMED - King Abdulaziz University; BAESHEN, NABIH - King Abdulaziz University; KYRPIDES, NIKOS - Department Of Energy Joint Genome

Submitted to: Standards in Genomic Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/21/2017
Publication Date: 3/4/2017
Citation: Reeve, W., Van Berkum, P., Ardley, J., Tian, R., Gollagher, M., Marinova, D., Elia, P.E., Reddy, T., Pillay, M., Varghese, N., Seshadri, R., Ivanova, N., Woyke, T., Baeshen, M.N., Baeshen, N.A., Kyrpides, N. 2017. High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr. Standards in Genomic Sciences. 12:26. doi: 10.1186/s40793-017-0238-2.

Interpretive Summary: Soybean, the second largest field crop in the U.S., can associate with Bradyrhizobium bacteria. The bacteria form nodules on the soybean roots and this is where nitrogen fixation occurs. This process naturally fertilizes the soybeans, and farmers can exploit this process to produce soybeans without adding topical fertilizer to farmlands. A better understanding of the Bradyrhizobium genes and DNA may help in understanding the factors influencing the bacteria and their association with soybeans and make for more efficient farming. In this investigation, the complete genome sequence of the specific bacterial species Bradyrhizobium elkanii was determined. A total of 9151 genes were identified, including those important for nitrogen fixation and association with soybeans. The availability of the complete genome sequence will be valuable in uncovering functions of all of the genes. These results will be useful to companies, universities and government laboratories that have the mission to improve soybean production, increase nitrogen fixation, and understand the association of soybeans with these specific bacteria.

Technical Abstract: Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), 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 76T was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the symbiotic abilities of B. elkanii USDA 76T are described, together with its genome sequence information and annotation. The 9,484,767 high-quality draft genome is arranged in 2 scaffolds of 25 contigs, containing 9,060 protein-coding genes and 91 RNA-only encoding genes. The B. elkanii USDA 76T 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 9,060 protein coding genes of USDA 76T were unique, including 22 genes of an intact resident prophage. A conserved set of 7,556 genes were also identified for this species, including genes encoding a general secretion pathway as well as type II, III, IV and VI secretion 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 76T 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 76T 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 76T to introduce various effector molecules into this host to enable nodulation.