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

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

doi:10.1186/s40793-015-0072-3

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

Journal Article · Fri Oct 16 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0072-3· OSTI ID:1256936

De Meyer, Sofie E. ^[1]; Tian, Rui ^[1]; Seshadri, Rekha ^[2]; Reddy, TBK ^[2]; Markowitz, Victor ^[3]; Ivanova, Natalia ^[2]; Pati, Amrita ^[2]; Woyke, Tanja ^[2]; Kyrpides, Nikos ^[4]; Yates, Ron ^[5]; Howieson, John ^[1]; Reeve, Wayne ^[1]

Murdoch Univ. (Australia)
DOE Joint Genome Inst., Walnut Creek, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
DOE Joint Genome Inst., Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
Murdoch Univ. (Australia); Dept. of Agriculture and Food, Western Australia (Australia)

Â© 2015 De Meyer et al. Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N 2 -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).

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

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

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

OSTI ID:: 1256936

Alternate ID(s):: OSTI ID: 1378594

Journal Information:: Standards in Genomic Sciences, Vol. 10, Issue 1; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 2 works

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References (35)

Improved Prediction of Signal Peptides: SignalP 3.0 Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795 https://doi.org/10.1016/j.jmb.2004.05.028	journal	July 2004
Burkholderia spp. are the most competitive symbionts of Mimosa , particularly under N-limited conditions Elliott, Geoffrey N.; Chou, Jui-Hsing; Chen, Wen-Ming Environmental Microbiology, Vol. 11, Issue 4 https://doi.org/10.1111/j.1462-2920.2008.01799.x	journal	April 2009
Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum Elliott, G. N.; Chen, W. -M.; Bontemps, C. Annals of Botany, Vol. 100, Issue 7 https://doi.org/10.1093/aob/mcm227	journal	September 2007
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
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment Ewing, Brent; Hillier, LaDeana; Wendl, Michael C. Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.175	journal	March 1998
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
Consed: A Graphical Tool for Sequence Finishing Gordon, David; Abajian, Chris; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.195	journal	March 1998
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen Krogh, Anders; Larsson, Björn; von Heijne, Gunnar Journal of Molecular Biology, Vol. 305, Issue 3 https://doi.org/10.1006/jmbi.2000.4315	journal	January 2001
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
Validation of publication of new names and new combinations previously effectively published outside the IJSEM Euzeby, Jean International Journal of Systematic and Evolutionary Microbiology, Vol. 55, Issue 6, p. 2235-2238 https://doi.org/10.1099/ijs.0.64108-0	journal	November 2005
A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey Reeve, Wayne; Ardley, Julie; Tian, Rui Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/1944-3277-10-14	journal	February 2015
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
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
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 Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata Pagani, I.; Liolios, K.; Jansson, J. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1100	journal	December 2011
The Genomic Standards Consortium Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy PLoS Biology, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pbio.1001088	journal	June 2011
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
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
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
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
Genome sequence of the Lebeckia ambigua-nodulating “Burkholderia sprentiae” strain WSM5005T Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason Standards in Genomic Sciences, Vol. 9, Issue 2 https://doi.org/10.4056/sigs.4558268	journal	December 2013
IMG 4 version of the integrated microbial genomes comparative analysis system Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt963	journal	October 2013
Root-nodule bacteria from indigenous legumes in the north-west of Western Australia and their interaction with exotic legumes Yates, R. Soil Biology and Biochemistry, Vol. 36, Issue 8 https://doi.org/10.1016/j.soilbio.2004.04.013	journal	August 2004
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S. PLoS ONE, Vol. 7, Issue 12 https://doi.org/10.1371/journal.pone.0048837	journal	December 2012
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities Ewing, Brent; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.186	journal	March 1998
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
Novel Burkholderia bacteria isolated from Lebeckia ambigua – A perennial suffrutescent legume of the fynbos Howieson, John G.; De Meyer, Sofie E.; Vivas-Marfisi, Anabel Soil Biology and Biochemistry, Vol. 60 https://doi.org/10.1016/j.soilbio.2013.01.009	journal	May 2013
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
Root-nodule bacteria from indigenous legumes in the north-west of Western Australia and their interaction with exotic legumes Yates, R. Soil Biology and Biochemistry https://doi.org/10.1016/s0038-0717(04)00130-0	journal	May 2004
Validation of publication of new names and new combinations previously effectively published outside the IJSEM International Journal of Systematic and Evolutionary Microbiology, Vol. 50, Issue 4, p. 1415-1417 https://doi.org/10.1099/00207713-50-4-1415	journal	July 2000
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
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
Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing Brofelth, Mattias; Ekstrand, Anna Isinger; Gour, Shashank Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-1068-0	journal	July 2020
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

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Symbiotic and non-symbiotic Paraburkholderia isolated from South African Lebeckia ambigua root nodules and the description of Paraburkholderia fynbosensis sp. nov. De Meyer, Sofie E.; Cnockaert, Margo; Moulin, Lionel International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 8 https://doi.org/10.1099/ijsem.0.002884	journal	August 2018
Members of the genus Burkholderia: good and bad guys Eberl, Leo; Vandamme, Peter F1000Research, Vol. 5 https://doi.org/10.12688/f1000research.8221.1	journal	January 2016
Members of the genus Burkholderia: good and bad guys Leo, Eberl,; Peter, Vandamme, Faculty of 1000 Ltd. https://doi.org/10.5167/uzh-131355	interactiveresource	January 2016

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