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Title: Genomic islands from five strains of Burkholderia pseudomallei

Abstract

Background: Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species. Results: We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described. Conclusion: Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIsmore » are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species.« less

Authors:
 [1];  [1];  [1];  [2];  [1];  [3];  [4];  [5];  [6];  [4];  [3];  [1];  [2]
+ Show Author Affiliations
  1. Northern Arizona Univ., Flagstaff, AZ (United States). Dept. of Biological Sciences
  2. Northern Arizona Univ., Flagstaff, AZ (United States). Dept. of Biological Sciences; The Translational Genomics Research Inst., Phoenix, AZ (United States)
  3. Charles Darwin Univ., Northern Territory (Australia). Menzies School of Health Research
  4. Mahidol Univ., Bangkok (Thailand). Mahidol-Oxford Research Unit
  5. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  6. J. Craig Venter Inst., Inc., Rockville, MD (United States); George Washington Univ., Washington, DC (United States)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1626473
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity

Citation Formats

Tuanyok, Apichai, Leadem, Benjamin R., Auerbach, Raymond K., Beckstrom-Sternberg, Stephen M., Beckstrom-Sternberg, James S., Mayo, Mark, Wuthiekanun, Vanaporn, Brettin, Thomas S., Nierman, William C., Peacock, Sharon J., Currie, Bart J., Wagner, David M., and Keim, Paul. Genomic islands from five strains of Burkholderia pseudomallei. United States: N. p., 2008. Web. doi:10.1186/1471-2164-9-566.
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Tuanyok, Apichai, Leadem, Benjamin R., Auerbach, Raymond K., Beckstrom-Sternberg, Stephen M., Beckstrom-Sternberg, James S., Mayo, Mark, Wuthiekanun, Vanaporn, Brettin, Thomas S., Nierman, William C., Peacock, Sharon J., Currie, Bart J., Wagner, David M., & Keim, Paul. Genomic islands from five strains of Burkholderia pseudomallei. United States. https://doi.org/10.1186/1471-2164-9-566
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Tuanyok, Apichai, Leadem, Benjamin R., Auerbach, Raymond K., Beckstrom-Sternberg, Stephen M., Beckstrom-Sternberg, James S., Mayo, Mark, Wuthiekanun, Vanaporn, Brettin, Thomas S., Nierman, William C., Peacock, Sharon J., Currie, Bart J., Wagner, David M., and Keim, Paul. Thu . "Genomic islands from five strains of Burkholderia pseudomallei". United States. https://doi.org/10.1186/1471-2164-9-566. https://www.osti.gov/servlets/purl/1626473.
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@article{osti_1626473,
title = {Genomic islands from five strains of Burkholderia pseudomallei},
author = {Tuanyok, Apichai and Leadem, Benjamin R. and Auerbach, Raymond K. and Beckstrom-Sternberg, Stephen M. and Beckstrom-Sternberg, James S. and Mayo, Mark and Wuthiekanun, Vanaporn and Brettin, Thomas S. and Nierman, William C. and Peacock, Sharon J. and Currie, Bart J. and Wagner, David M. and Keim, Paul},
abstractNote = {Background: Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species. Results: We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described. Conclusion: Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species.},
doi = {10.1186/1471-2164-9-566},
journal = {BMC Genomics},
number = 1,
volume = 9,
place = {United States},
year = {Thu Nov 27 00:00:00 EST 2008},
month = {Thu Nov 27 00:00:00 EST 2008}
}
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Circular genome visualization and exploration using CGView
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The Epidemiology of Melioidosis in Ubon Ratchatani, Northeast Thailand
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  • Emerging Infectious Diseases, Vol. 11, Issue 4
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