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

Abstract

Bradyrhizobium elkanii USDA 76 T (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 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 pathwaymore » 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.« less

Authors:
 [1];  [2]; ORCiD logo [1];  [1];  [3];  [3];  [2];  [4];  [5];  [4];  [4];  [4];  [4];  [6];  [7];  [8]
  1. Murdoch Univ., WA (Australia). School of Veterinary and Life Sciences
  2. Beltsville Agricultural Research Center, MD (United States)
  3. Curtin Univ., Bentley, WA (Australia). Sustainability Policy Inst.
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
  6. Univ. of Jeddah (Saudi Arabia). Dept. of Biology
  7. King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379762
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; root-nodule bacteria; GEBA-RNB; nitrogen fixation; bradyrhizobium; soybean; type III secretion system

Citation Formats

Reeve, Wayne, van Berkum, Peter, Ardley, Julie, Tian, Rui, Gollagher, Margaret, Marinova, Dora, Elia, Patrick, Reddy, T. B. K., Pillay, Manoj, Varghese, Neha, Seshadri, Rekha, Ivanova, Natalia, Woyke, Tanja, Baeshen, Mohamed N., Baeshen, Nabih A., and Kyrpides, Nikos. High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0238-2.
Reeve, Wayne, van Berkum, Peter, Ardley, Julie, Tian, Rui, Gollagher, Margaret, Marinova, Dora, Elia, Patrick, Reddy, T. B. K., Pillay, Manoj, Varghese, Neha, Seshadri, Rekha, Ivanova, Natalia, Woyke, Tanja, Baeshen, Mohamed N., Baeshen, Nabih A., & Kyrpides, Nikos. High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr. United States. doi:10.1186/s40793-017-0238-2.
Reeve, Wayne, van Berkum, Peter, Ardley, Julie, Tian, Rui, Gollagher, Margaret, Marinova, Dora, Elia, Patrick, Reddy, T. B. K., Pillay, Manoj, Varghese, Neha, Seshadri, Rekha, Ivanova, Natalia, Woyke, Tanja, Baeshen, Mohamed N., Baeshen, Nabih A., and Kyrpides, Nikos. Sat . "High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr". United States. doi:10.1186/s40793-017-0238-2. https://www.osti.gov/servlets/purl/1379762.
@article{osti_1379762,
title = {High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr},
author = {Reeve, Wayne and van Berkum, Peter and Ardley, Julie and Tian, Rui and Gollagher, Margaret and Marinova, Dora and Elia, Patrick and Reddy, T. B. K. and Pillay, Manoj and Varghese, Neha and Seshadri, Rekha and Ivanova, Natalia and Woyke, Tanja and Baeshen, Mohamed N. and Baeshen, Nabih A. and Kyrpides, Nikos},
abstractNote = {Bradyrhizobium elkanii USDA 76 T (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 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.},
doi = {10.1186/s40793-017-0238-2},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {2017},
month = {3}
}

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    Works referencing / citing this record:

    High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr [Supplemental Data]
    dataset, March 2017

    • Reeve, Wayne; van Berkum, Peter; Ardley, Julie
    • figshare-Supplementary information for journal article at DOI: 10.1186/s40793-017-0238-2, 2 DOCX files
    • DOI: 10.6084/m9.figshare.c.3709285