title: High-quality permanent draft genome sequence of theBradyrhizobium elkaniitype strain USDA 76T, isolated fromGlycine max(L.) Merr.
abstract: Bradyrhizobium elkaniiUSDA 76T(INSCD = ARAG00000000), the type strain forBradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule ofGlycine max(L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume,B. elkaniiUSDA 76Twas selected as part of the DOE Joint Genome Institute 2010Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteriasequencing project. Here the symbiotic abilities ofB. elkaniiUSDA 76Tare 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. TheB. elkaniiUSDA 76Tgenome contains a low GC content region with symbioticnodandfixgenes, indicating the presence of a symbiotic island integration. A comparison of fiveB. elkaniigenomes that formed a clique revealed that 356 of the 9060 protein coding genes of USDA 76Twere 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 forRjand/orrjsoybean cultivars. Here we show that the USDA 76Tgenome 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 76Twas 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 76Tto introduce various effector molecules into this host to enable nodulation.
authors.affiliation: School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia.
authors.forename: Wayne
authors.initials: W
authors.lastname: Reeve
authors.affiliation: U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA.
authors.forename: Peter
authors.initials: P
authors.lastname: van Berkum
authors.affiliation: School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia.
authors.forename: Julie
authors.identifier: 0000-0001-9938-606X
authors.initials: J
authors.lastname: Ardley
authors.affiliation: School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia.
authors.forename: Rui
authors.initials: R
authors.lastname: Tian
authors.affiliation: Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia.
authors.forename: Margaret
authors.initials: M
authors.lastname: Gollagher
authors.affiliation: Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia.
authors.forename: Dora
authors.initials: D
authors.lastname: Marinova
authors.affiliation: U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Elia
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: T B K
authors.initials: TBK
authors.lastname: Reddy
authors.affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.
authors.forename: Manoj
authors.initials: M
authors.lastname: Pillay
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Neha
authors.initials: N
authors.lastname: Varghese
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Rekha
authors.initials: R
authors.lastname: Seshadri
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia.
authors.forename: Mohamed N
authors.initials: MN
authors.lastname: Baeshen
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Nabih A
authors.initials: NA
authors.lastname: Baeshen
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.|Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
keywords: Bradyrhizobium; GEBA-RNB; Nitrogen fixation; Root-nodule bacteria; Soybean; Type III secretion system