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Title: High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy

Abstract

Rhizobium sullae strain WSM1592 is an aerobic, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule formed on the short-lived perennial legume Hedysarum coronarium (also known as Sulla coronaria or Sulla). WSM1592 was isolated from a nodule recovered from H. coronarium roots located in Ottava, bordering Sassari, Sardinia in 1995. WSM1592 is highly effective at fixing nitrogen with H. coronarium, and is currently the commercial Sulla inoculant strain in Australia. Here we describe the features of R. sullae strain WSM1592, together with genome sequence information and its annotation. The 7,530,820 bp high-quality permanent draft genome is arranged into 118 scaffolds of 118 contigs containing 7.453 protein-coding genes and 73 RNA-only encoding genes. In conclusion, this rhizobial genome is sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Authors:
 [1];  [2];  [2];  [2];  [3];  [3];  [3];  [4];  [3];  [5];  [6];  [6];  [7];  [8];  [2]
  1. Dept. of Agriculture and Food, Western Australia (Australia); Murdoch Univ., Western Australia (Australia)
  2. Murdoch Univ., Western Australia (Australia)
  3. DOE Joint Genome Inst., Walnut Creek, CA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. DOE Joint Genome Inst., Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  6. Dept. of Agriculture and Food, Western Australia (Australia)
  7. Univ. of Sassari, Sardinia (Italy)
  8. National Research Council (CNR), Sassari (Italy). Inst. for the Animal Production System in the Mediterranean Environment (ISPAAM)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1256922
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; 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; Nitrogen fixation; Rhizobia; Alphaproteobacteria; GEBA-RNB

Citation Formats

Yates, Ron, Howieson, John, De Meyer, Sofie E., Tian, Rui, Seshadri, Rekha, Pati, Amrita, Woyke, Tanja, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Loi, Angelo, Nutt, Brad, Garau, Giovanni, Sulas, Leonardo, and Reeve, Wayne. High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy. United States: N. p., 2015. Web. doi:10.1186/s40793-015-0020-2.
Yates, Ron, Howieson, John, De Meyer, Sofie E., Tian, Rui, Seshadri, Rekha, Pati, Amrita, Woyke, Tanja, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Loi, Angelo, Nutt, Brad, Garau, Giovanni, Sulas, Leonardo, & Reeve, Wayne. High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy. United States. https://doi.org/10.1186/s40793-015-0020-2
Yates, Ron, Howieson, John, De Meyer, Sofie E., Tian, Rui, Seshadri, Rekha, Pati, Amrita, Woyke, Tanja, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Loi, Angelo, Nutt, Brad, Garau, Giovanni, Sulas, Leonardo, and Reeve, Wayne. Fri . "High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy". United States. https://doi.org/10.1186/s40793-015-0020-2. https://www.osti.gov/servlets/purl/1256922.
@article{osti_1256922,
title = {High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy},
author = {Yates, Ron and Howieson, John and De Meyer, Sofie E. and Tian, Rui and Seshadri, Rekha and Pati, Amrita and Woyke, Tanja and Markowitz, Victor and Ivanova, Natalia and Kyrpides, Nikos and Loi, Angelo and Nutt, Brad and Garau, Giovanni and Sulas, Leonardo and Reeve, Wayne},
abstractNote = {Rhizobium sullae strain WSM1592 is an aerobic, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule formed on the short-lived perennial legume Hedysarum coronarium (also known as Sulla coronaria or Sulla). WSM1592 was isolated from a nodule recovered from H. coronarium roots located in Ottava, bordering Sassari, Sardinia in 1995. WSM1592 is highly effective at fixing nitrogen with H. coronarium, and is currently the commercial Sulla inoculant strain in Australia. Here we describe the features of R. sullae strain WSM1592, together with genome sequence information and its annotation. The 7,530,820 bp high-quality permanent draft genome is arranged into 118 scaffolds of 118 contigs containing 7.453 protein-coding genes and 73 RNA-only encoding genes. In conclusion, this rhizobial genome is sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.},
doi = {10.1186/s40793-015-0020-2},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {Fri Jul 24 00:00:00 EDT 2015},
month = {Fri Jul 24 00:00:00 EDT 2015}
}

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  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
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journal, June 2009


tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007

  • Pruesse, E.; Quast, C.; Knittel, K.
  • Nucleic Acids Research, Vol. 35, Issue 21
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Rhizobium sullae sp. nov. (formerly 'Rhizobium hedysari'), the root-nodule microsymbiont of Hedysarum coronarium L.
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R Factor Transfer in Rhizobium leguminosarum
journal, September 1974


Rhizobium sullae sp. nov. (formerly 'Rhizobium hedysari'), the root-nodule microsymbiont of Hedysarum coronarium L
journal, July 2002

  • Squartini, A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 52, Issue 4
  • DOI: 10.1099/ijs.0.01821-0

Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
journal, November 2011

  • Kim, O. -S.; Cho, Y. -J.; Lee, K.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue Pt 3
  • DOI: 10.1099/ijs.0.038075-0

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey
journal, February 2015

  • Reeve, Wayne; Ardley, Julie; Tian, Rui
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/1944-3277-10-14

Nitrogen Fixation of Sulla under Mediterranean Conditions
journal, November 2009

  • Sulas, Leonardo; Seddaiu, Giovanna; Muresu, Rosella
  • Agronomy Journal, Vol. 101, Issue 6
  • DOI: 10.2134/agronj2009.0151

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009

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Works referencing / citing this record:

Genome Sequence of Rhizobium sullae HCNT1 Isolated from Hedysarum coronarium Nodules and Featuring Peculiar Denitrification Phenotypes
journal, January 2018


Inoculation and N Fertilization Affect the Dry Matter, N Fixation, and Bioactive Compounds in Sulla Leaves
journal, June 2019