Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia

Walker, Robert; Watkin, Elizabeth; Tian, Rui; Bräu, Lambert; O’Hara, Graham; Goodwin, Lynne; Han, James; Lobos, Elizabeth; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

doi:10.4056/sigs.5008793

Title: Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia

Journal Article · Tue Dec 31 00:00:00 EST 2013 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.5008793· OSTI ID:1628691

Walker, Robert ^[1]; Watkin, Elizabeth ^[1]; Tian, Rui ^[2]; Bräu, Lambert ^[3]; O’Hara, Graham ^[2]; Goodwin, Lynne ^[4]; Han, James ^[5]; Lobos, Elizabeth ^[5]; Huntemann, Marcel ^[5]; Pati, Amrita ^[5]; Woyke, Tanja ^[5]; Mavromatis, Konstantinos ^[5]; Markowitz, Victor ^[6]; Ivanova, Natalia ^[5]; Kyrpides, Nikos ^[5]; Reeve, Wayne ^[7]

Curtain Univ., WA (Australia). Faculty of Health Sciences. School of Biomedical Sciences
Murdoch Univ., WA (Australia). School of Veterinary and Life Sciences. Centre for Rhizobium Studies
Deakin Univ., Victoria (Australia). School of Life and Environmental Sciences
Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Bioscience Division
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
Murdoch Univ., WA (Australia). School of Veterinary and Life Sciences. 2 Centre for Rhizobium Studies

Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod isolated from acidic soil collected in 2001 from Karijini National Park, Western Australia, using Kennedia coccinea (Coral Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K. coccinea, but subsequently lost symbiotic competence. Here we describe the features of Burkholderia sp. strain WSM2230, together with genome sequence information and its annotation. The 6,309,801 bp high-quality-draft genome is arranged into 33 scaffolds of 33 contigs containing 5,590 protein-coding genes and 63 RNA-only encoding genes. The genome sequence of WSM2230 failed to identify nodulation genes and provides an explanation for the observed failure of the laboratory grown strain to nodulate. The genome of this strain is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-06NA25396; AC02-05CH11231; AC52-07NA27344

OSTI ID:: 1628691

Journal Information:: Standards in Genomic Sciences, Vol. 9, Issue 3; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (32)

Diversity and occurrence of Burkholderia spp. in the natural environment Compant, Stéphane; Nowak, Jerzy; Coenye, Tom FEMS Microbiology Reviews, Vol. 32, Issue 4 https://doi.org/10.1111/j.1574-6976.2008.00113.x	journal	July 2008
Novel strains of nodulating Burkholderia have a role in nitrogen fixation with papilionoid herbaceous legumes adapted to acid, infertile soils Garau, Giovanni; Yates, Ron J.; Deiana, Pietrino Soil Biology and Biochemistry, Vol. 41, Issue 1 https://doi.org/10.1016/j.soilbio.2008.10.011	journal	January 2009
Symbiotic Effectiveness of Rhizobial Mutualists Varies in Interactions with Native Australian Legume Genera Thrall, Peter H.; Laine, Anna-Liisa; Broadhurst, Linda M. PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0023545	journal	August 2011
Genetic characterization of root-nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia Hoque, Mohammad S.; Broadhurst, Linda M.; Thrall, Peter H. International Journal of Systematic and Evolutionary Microbiology, Vol. 61, Issue 2 https://doi.org/10.1099/ijs.0.021014-0	journal	February 2011
Nodulation and effective nitrogen fixation of Macroptilium atropurpureum (siratro) by Burkholderia tuberum, a nodulating and plant growth promoting beta-proteobacterium, are influenced by environmental factors Angus, Annette A.; Lee, Andrew; Lum, Michelle R. Plant and Soil, Vol. 369, Issue 1-2 https://doi.org/10.1007/s11104-013-1590-7	journal	January 2013
The diversity and biogeography of soil bacterial communities Fierer, N.; Jackson, R. B. Proceedings of the National Academy of Sciences, Vol. 103, Issue 3 https://doi.org/10.1073/pnas.0507535103	journal	January 2006
Selection for acid tolerance inRhizobium meliloti Howieson, J. G.; Ewing, M. A.; D'Antuono, M. F. Plant and Soil, Vol. 105, Issue 2 https://doi.org/10.1007/BF02376781	journal	September 1988
R Factor Transfer in Rhizobium leguminosarum Beringer, J. E. Microbiology, Vol. 84, Issue 1 https://doi.org/10.1099/00221287-84-1-188	journal	September 1974
The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB Trujillo, Martha E. International Journal of Systematic and Evolutionary Microbiology https://doi.org/10.1099/00207713-43-2-398	journal	April 1993
Proposal of Burkholderia gen. nov. and Transfer of Seven Species of the Genus Pseudomonas Homology Group II to the New Genus, with the Type Species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Yabuuchi, Eiko; Kosako, Yoshimasa; Oyaizu, Hiroshi Microbiology and Immunology, Vol. 36, Issue 12 https://doi.org/10.1111/j.1348-0421.1992.tb02129.x	journal	December 1992
Polyphasic Taxonomy in the Genus Burkholderia Leading to an Emended Description of the Genus and Proposition of Burkholderia vietnamiensis sp. nov. for N2-Fixing Isolates from Rice in Vietnam Gillis, M.; Van Van, T.; Bardin, R. International Journal of Systematic Bacteriology, Vol. 45, Issue 2 https://doi.org/10.1099/00207713-45-2-274	journal	April 1995
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Tamura, K.; Peterson, D.; Peterson, N. Molecular Biology and Evolution, Vol. 28, Issue 10 https://doi.org/10.1093/molbev/msr121	journal	May 2011
Confidence Limits on Phylogenies: An Approach Using the Bootstrap Felsenstein, Joseph Evolution, Vol. 39, Issue 4, p. 783-791 https://doi.org/10.2307/2408678	journal	July 1985
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata Liolios, K.; Mavromatis, K.; Tavernarakis, N. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm884	journal	December 2007
Constructs for insertional mutagenesis, transcriptional signal localization and gene regulation studies in root nodule and other bacteria Reeve, W. G.; Tiwari, R. P.; Worsley, P. S. Microbiology, Vol. 145, Issue 6 https://doi.org/10.1099/13500872-145-6-1307	journal	June 1999
Solexa Ltd Bennett, Simon Pharmacogenomics, Vol. 5, Issue 4 https://doi.org/10.1517/14622416.5.4.433	journal	June 2004
High-quality draft assemblies of mammalian genomes from massively parallel sequence data Gnerre, S.; MacCallum, I.; Przybylski, D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 4 https://doi.org/10.1073/pnas.1017351108	journal	December 2010
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A. Standards in Genomic Sciences, Vol. 1, Issue 1 https://doi.org/10.4056/sigs.632	journal	July 2009
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia Nature Methods, Vol. 7, Issue 6 https://doi.org/10.1038/nmeth.1457	journal	May 2010
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.0955	journal	March 1997
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Pruesse, E.; Quast, C.; Knittel, K. Nucleic Acids Research, Vol. 35, Issue 21 https://doi.org/10.1093/nar/gkm864	journal	November 2007
IMG ER: a system for microbial genome annotation expert review and curation Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N. Bioinformatics, Vol. 25, Issue 17 https://doi.org/10.1093/bioinformatics/btp393	journal	June 2009
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass Xu, Xiaoheng; Feng, Guangyan; Huang, Linkai Molecular Biology Reports, Vol. 47, Issue 3 https://doi.org/10.1007/s11033-020-05279-9	journal	February 2020
Genetic diversity of Amomum xanthioides and its related species from Southeast Asia and China Sone, Mikako; Zhu, Shu; Cheng, Xiao Journal of Natural Medicines, Vol. 75, Issue 4 https://doi.org/10.1007/s11418-021-01512-2	journal	May 2021
Dietary palmitic acid promotes a prometastatic memory via Schwann cells Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc Nature, Vol. 599, Issue 7885 https://doi.org/10.1038/s41586-021-04075-0	journal	November 2021
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.955	journal	March 1997
Burkholderia species are ancient symbionts of legumes Bontemps, Cyril; Elliott, Geoffrey N.; Simon, Marcelo F. Molecular Ecology, Vol. 19, Issue 1 https://doi.org/10.1111/j.1365-294x.2009.04458.x	journal	January 2010
Insights into the history of the legume-betaproteobacterial symbiosis Angus, Annette A.; Hirsch, Ann M. Molecular Ecology, Vol. 19, Issue 1 https://doi.org/10.1111/j.1365-294x.2009.04459.x	journal	January 2010

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