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Title: High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176

Abstract

We report that Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in October 2007. This plant persists in infertile, acidic and deep sandy soils, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. Here we describe the features of Burkholderia sp. strain WSM4176, which represents a potential inoculant quality strain for L. ambigua, together with sequence and annotation. The 9,065,247 bp high-quality-draft genome is arranged in 13 scaffolds of 65 contigs, contains 8369 protein-coding genes and 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal (Project ID 882).

Authors:
 [1];  [1];  [2];  [2];  [3];  [2];  [2];  [2];  [4];  [5];  [1];  [1]
  1. Murdoch Univ. (Australia)
  2. DOE Joint Genome Inst., Walnut Creek, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. DOE Joint Genome Inst., Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  5. Murdoch Univ. (Australia); Dept. of Agriculture and Food, Western Australia (Australia)
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:
1256936
Alternate Identifier(s):
OSTI ID: 1378594
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; Betaproteobacteria; GEBA-RNB

Citation Formats

De Meyer, Sofie E., Tian, Rui, Seshadri, Rekha, Reddy, TBK, Markowitz, Victor, Ivanova, Natalia, Pati, Amrita, Woyke, Tanja, Kyrpides, Nikos, Yates, Ron, Howieson, John, and Reeve, Wayne. High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176. United States: N. p., 2015. Web. doi:10.1186/s40793-015-0072-3.
De Meyer, Sofie E., Tian, Rui, Seshadri, Rekha, Reddy, TBK, Markowitz, Victor, Ivanova, Natalia, Pati, Amrita, Woyke, Tanja, Kyrpides, Nikos, Yates, Ron, Howieson, John, & Reeve, Wayne. High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176. United States. doi:10.1186/s40793-015-0072-3.
De Meyer, Sofie E., Tian, Rui, Seshadri, Rekha, Reddy, TBK, Markowitz, Victor, Ivanova, Natalia, Pati, Amrita, Woyke, Tanja, Kyrpides, Nikos, Yates, Ron, Howieson, John, and Reeve, Wayne. Fri . "High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176". United States. doi:10.1186/s40793-015-0072-3. https://www.osti.gov/servlets/purl/1256936.
@article{osti_1256936,
title = {High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176},
author = {De Meyer, Sofie E. and Tian, Rui and Seshadri, Rekha and Reddy, TBK and Markowitz, Victor and Ivanova, Natalia and Pati, Amrita and Woyke, Tanja and Kyrpides, Nikos and Yates, Ron and Howieson, John and Reeve, Wayne},
abstractNote = {We report that Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in October 2007. This plant persists in infertile, acidic and deep sandy soils, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. Here we describe the features of Burkholderia sp. strain WSM4176, which represents a potential inoculant quality strain for L. ambigua, together with sequence and annotation. The 9,065,247 bp high-quality-draft genome is arranged in 13 scaffolds of 65 contigs, contains 8369 protein-coding genes and 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal (Project ID 882).},
doi = {10.1186/s40793-015-0072-3},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {2015},
month = {10}
}

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Works referenced in this record:

Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004

  • Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
  • Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
  • DOI: 10.1016/j.jmb.2004.05.028

Burkholderia spp. are the most competitive symbionts of Mimosa , particularly under N-limited conditions
journal, April 2009


Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum
journal, September 2007

  • Elliott, G. N.; Chen, W. -M.; Bontemps, C.
  • Annals of Botany, Vol. 100, Issue 7
  • DOI: 10.1093/aob/mcm227

Selection for acid tolerance inRhizobium meliloti
journal, September 1988

  • Howieson, J. G.; Ewing, M. A.; D'Antuono, M. F.
  • Plant and Soil, Vol. 105, Issue 2
  • DOI: 10.1007/BF02376781

Base-Calling of Automated Sequencer Traces Using Phred.  I. Accuracy Assessment
journal, March 1998

  • Ewing, Brent; Hillier, LaDeana; Wendl, Michael C.
  • Genome Research, Vol. 8, Issue 3
  • DOI: 10.1101/gr.8.3.175

High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010

  • Gnerre, S.; MacCallum, I.; Przybylski, D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1017351108

Consed: A Graphical Tool for Sequence Finishing
journal, March 1998

  • Gordon, David; Abajian, Chris; Green, Phil
  • Genome Research, Vol. 8, Issue 3
  • DOI: 10.1101/gr.8.3.195

Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001

  • Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
  • Journal of Molecular Biology, Vol. 305, Issue 3
  • DOI: 10.1006/jmbi.2000.4315

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
journal, May 2011

  • Tamura, K.; Peterson, D.; Peterson, N.
  • Molecular Biology and Evolution, Vol. 28, Issue 10
  • DOI: 10.1093/molbev/msr121

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

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

R Factor Transfer in Rhizobium leguminosarum
journal, September 1974


The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011

  • Pagani, I.; Liolios, K.; Jansson, J.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1100

The Genomic Standards Consortium
journal, June 2011


Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

  • Woese, C. R.; Kandler, O.; Wheelis, M. L.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
  • DOI: 10.1073/pnas.87.12.4576

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


Novel strains of nodulating Burkholderia have a role in nitrogen fixation with papilionoid herbaceous legumes adapted to acid, infertile soils
journal, January 2009


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


Genome sequence of the Lebeckia ambigua-nodulating “Burkholderia sprentiae” strain WSM5005T
journal, December 2013

  • Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason
  • Standards in Genomic Sciences, Vol. 9, Issue 2
  • DOI: 10.4056/sigs.4558268

IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt963

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012


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


Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998


IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009


Novel Burkholderia bacteria isolated from Lebeckia ambigua – A perennial suffrutescent legume of the fynbos
journal, May 2013


GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010

  • Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth.1457