Genomic islands from five strains of Burkholderia pseudomallei

Apichai Tuanyok, Benjamin R. Leadem, Raymond K. Auerbach, Stephen M Beckstrom-Sternberg, James S. Beckstrom-Sternberg, Mark Mayo, Vanaporn Wuthiekanun, Thomas S. Brettin, William C. Nierman, Sharon J. Peacock, Bart J. Currie, David M Wagner, Paul S Keim

Research output: Contribution to journalArticle

59 Citations (Scopus)

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 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.

Original languageEnglish (US)
Article number566
JournalBMC Genomics
Volume9
DOIs
StatePublished - Nov 27 2008

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Burkholderia pseudomallei
Genomic Islands
Transfer RNA
Melioidosis
Interspersed Repetitive Sequences
Terminology
Genetic Recombination
Genes
Genome
Morbidity

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Genomic islands from five strains of Burkholderia pseudomallei. / 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 S.

In: BMC Genomics, Vol. 9, 566, 27.11.2008.

Research output: Contribution to journalArticle

Tuanyok, A, Leadem, BR, Auerbach, RK, Beckstrom-Sternberg, SM, Beckstrom-Sternberg, JS, Mayo, M, Wuthiekanun, V, Brettin, TS, Nierman, WC, Peacock, SJ, Currie, BJ, Wagner, DM & Keim, PS 2008, 'Genomic islands from five strains of Burkholderia pseudomallei', BMC Genomics, vol. 9, 566. https://doi.org/10.1186/1471-2164-9-566
Tuanyok A, Leadem BR, Auerbach RK, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, Mayo M et al. Genomic islands from five strains of Burkholderia pseudomallei. BMC Genomics. 2008 Nov 27;9. 566. https://doi.org/10.1186/1471-2164-9-566
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 S. / Genomic islands from five strains of Burkholderia pseudomallei. In: BMC Genomics. 2008 ; Vol. 9.
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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 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.",
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AU - Leadem, Benjamin R.

AU - Auerbach, Raymond K.

AU - Beckstrom-Sternberg, Stephen M

AU - Beckstrom-Sternberg, James S.

AU - Mayo, Mark

AU - Wuthiekanun, Vanaporn

AU - Brettin, Thomas S.

AU - Nierman, William C.

AU - Peacock, Sharon J.

AU - Currie, Bart J.

AU - Wagner, David M

AU - Keim, Paul S

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N2 - 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.

AB - 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.

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