Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6

D'haeseleer, Patrik; Johnson, Shannon L.; Davenport, Karen W.; Chain, Patrick S.; Schoeniger, Joe; Ray, Debjit; Sinha, Anupama; Williams, Kelly P.; Peña, José; Branda, Steven S.; El-Etr, Sahar

doi:10.1128/genomeA.00649-16

Title: Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6

Journal Article · Thu Jun 30 00:00:00 EDT 2016 · Genome Announcements

DOI:https://doi.org/10.1128/genomeA.00649-16· OSTI ID:1786402

^[1];

^[2]; Davenport, Karen W. ^[2]; Chain, Patrick S. ^[2]; Schoeniger, Joe ^[3]; Ray, Debjit ^[3]; Sinha, Anupama ^[3]; Williams, Kelly P. ^[3]; Peña, José ^[1]; Branda, Steven S. ^[3]; El-Etr, Sahar ^[1]

Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
Los Alamos National Laboratory (LANL), Los Alamos, New Mexico, USA
Sandia National Laboratories (SNL), Livermore, California, USA

We present the draft genome sequence ofBurkholderia pseudomalleiPHLS 6, a virulent clinical strain isolated from a melioidosis patient in Bangladesh in 1960. This draft genome consists of 39 contigs and is 7,322,181 bp long.

View Journal Article

Cite

Export

Save

Research Organization:: Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: 15-ERD-017; AC04-94AL85000

OSTI ID:: 1786402

Alternate ID(s):: OSTI ID: 1303160

Report Number(s):: SAND2016-4716J; e00649-16

Journal Information:: Genome Announcements, Journal Name: Genome Announcements Vol. 4 Journal Issue: 3; ISSN 2169-8287

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (29)

Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping U'Ren, Jana M.; Schupp, James M.; Pearson, Talima BMC Microbiology, Vol. 7, Issue 1 https://doi.org/10.1186/1471-2180-7-23	journal	January 2007
An Ergatis-based prokaryotic genome annotation web server Hemmerich, Chris; Buechlein, Aaron; Podicheti, Ram Bioinformatics, Vol. 26, Issue 8 https://doi.org/10.1093/bioinformatics/btq090	journal	March 2010
Melioidosis Wiersinga, W. Joost; Currie, Bart J.; Peacock, Sharon J. New England Journal of Medicine, Vol. 367, Issue 11 https://doi.org/10.1056/NEJMra1204699	journal	September 2012
Bridger: a new framework for de novo transcriptome assembly using RNA-seq data Chang, Zheng; Li, Guojun; Liu, Juntao Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0596-2	journal	February 2015
Simple sequence repeat (SSR)-based gene diversity in Burkholderia pseudomallei and Burkholderia mallei Song, Han; Hwang, Junghyun; Myung, Jaehee Molecules and Cells, Vol. 27, Issue 2 https://doi.org/10.1007/s10059-009-0029-8	journal	February 2009
Melioidosis: insights into the pathogenicity of Burkholderia pseudomallei Wiersinga, W. Joost; van der Poll, Tom; White, Nicholas J. Nature Reviews Microbiology, Vol. 4, Issue 4 https://doi.org/10.1038/nrmicro1385	journal	April 2006
The Core and Accessory Genomes of Burkholderia pseudomallei: Implications for Human Melioidosis Sim, Siew Hoon; Yu, Yiting; Lin, Chi Ho PLoS Pathogens, Vol. 4, Issue 10 https://doi.org/10.1371/journal.ppat.1000178	journal	October 2008
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry Journal of Computational Biology, Vol. 19, Issue 5 https://doi.org/10.1089/cmb.2012.0021	journal	May 2012
ALLPATHS: De novo assembly of whole-genome shotgun microreads Butler, J.; MacCallum, I.; Kleber, M. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.7337908	journal	February 2008
Workshop on Treatment of and Postexposure Prophylaxis for Burkholderia pseudomallei and B. mallei Infection, 2010 Lipsitz, Rebecca; Garges, Susan; Aurigemma, Rosemarie Emerging Infectious Diseases, Vol. 18, Issue 12 https://doi.org/10.3201/eid1812.120638	journal	December 2012
Patterns of large-scale genomic variation in virulent and avirulent Burkholderia species Ong, C. Genome Research, Vol. 14, Issue 11 https://doi.org/10.1101/gr.1608904	journal	November 2004
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
Public Health Assessment of Potential Biological Terrorism Agents Rotz, Lisa D. Emerging Infectious Diseases, Vol. 8, Issue 2 https://doi.org/10.3201/eid0802.010164	journal	February 2002
Burkholderia pseudomallei genome plasticity associated with genomic island variation Tumapa, Sarinna; Holden, Matthew TG; Vesaratchavest, Mongkol BMC Genomics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2164-9-190	journal	January 2008
Within-Host Evolution of Burkholderia pseudomallei in Four Cases of Acute Melioidosis Price, Erin P.; Hornstra, Heidie M.; Limmathurotsakul, Direk PLoS Pathogens, Vol. 6, Issue 1 https://doi.org/10.1371/journal.ppat.1000725	journal	January 2010
Microevolution of Burkholderia pseudomallei during an Acute Infection Limmathurotsakul, Direk; Holden, Matthew T. G.; Coupland, Paul Journal of Clinical Microbiology, Vol. 52, Issue 9 https://doi.org/10.1128/JCM.01219-14	journal	June 2014
NxTrim: optimized trimming of Illumina mate pair reads: Table 1. O’Connell, Jared; Schulz-Trieglaff, Ole; Carlson, Emma Bioinformatics, Vol. 31, Issue 12 https://doi.org/10.1093/bioinformatics/btv057	journal	February 2015
Integrative Genomic, Transcriptional, and Proteomic Diversity in Natural Isolates of the Human Pathogen Burkholderia pseudomallei Ou, Keli; Ong, Catherine; Koh, Shze Yung Journal of Bacteriology, Vol. 187, Issue 12 https://doi.org/10.1128/JB.187.12.4276-4285.2005	journal	June 2005
Increasing Incidence of Human Melioidosis in Northeast Thailand Wongratanacheewin, Surasakdi; Day, Nicholas P. J.; Teerawattanasook, Nittaya The American Journal of Tropical Medicine and Hygiene, Vol. 82, Issue 6 https://doi.org/10.4269/ajtmh.2010.10-0038	journal	June 2010
The Epidemiology and Clinical Spectrum of Melioidosis: 540 Cases from the 20 Year Darwin Prospective Study Currie, Bart J.; Ward, Linda; Cheng, Allen C. PLoS Neglected Tropical Diseases, Vol. 4, Issue 11 https://doi.org/10.1371/journal.pntd.0000900	journal	November 2010
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Overbeek, Ross; Olson, Robert; Pusch, Gordon D. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1226	journal	November 2013
Biological warfare agents Thavaselvam, Duraipandian; Vijayaraghavan, Rajagopalan Journal of Pharmacy and Bioallied Sciences, Vol. 2, Issue 3 https://doi.org/10.4103/0975-7406.68499	journal	January 2010
Predicted global distribution of Burkholderia pseudomallei and burden of melioidosis Limmathurotsakul, Direk; Golding, Nick; Dance, David A. B. Nature Microbiology, Vol. 1, Issue 1 https://doi.org/10.1038/nmicrobiol.2015.8	journal	January 2016
Halving of Mortality of Severe Melioidosis by Ceftazidime White, N. J.; Chaowagul, W.; Wuthiekanun, V. The Lancet, Vol. 334, Issue 8665 https://doi.org/10.1016/S0140-6736(89)90768-X	journal	September 1989
Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei Holden, M. T. G.; Titball, R. W.; Peacock, S. J. Proceedings of the National Academy of Sciences, Vol. 101, Issue 39 https://doi.org/10.1073/pnas.0403302101	journal	September 2004
Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts Romero, Claudia M.; DeShazer, David; Feldblyum, Tamara BMC Genomics, Vol. 7, Issue 1 https://doi.org/10.1186/1471-2164-7-228	journal	September 2006
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
GapFiller: a de novo assembly approach to fill the gap within paired reads Nadalin, Francesca; Vezzi, Francesco; Policriti, Alberto BMC Bioinformatics, Vol. 13, Issue S14 https://doi.org/10.1186/1471-2105-13-S14-S8	journal	September 2012

Similar Records

Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei

Journal Article · Thu Feb 12 00:00:00 EST 2015 · Genome Announcements · OSTI ID:1786402

Johnson, Shannon L.; Baker, Anthony L.; Chain, Patrick S.; +13 more

Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates

Journal Article · Tue Dec 23 00:00:00 EST 2014 · PLoS ONE · OSTI ID:1786402

Challacombe, Jean F.; Stubben, Chris J.; Klimko, Christopher P.; +7 more

Complete Genome Sequence of the Encephalomyelitic Burkholderia pseudomallei Strain MSHR305

Journal Article · Thu Jun 27 00:00:00 EDT 2013 · Genome Announcements · OSTI ID:1786402

Stone, J. K.; Johnson, S. L.; Bruce, D. C.; +6 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6

Citation Formats

References (29)

Similar Records

Related Subjects