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Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates

Spring-Pearson, Senanu M., Stone, Joshua K., Doyle, Adina, Allender, Christopher J., Okinaka, Richard T., Mayo, Mark J., Broomall, Stacey M., Hill, Jessica M., Karavis, Mark A., Hubbard, Kyle S., Insalaco, Joseph M., McNew, Lauren A., Rosenzweig, C. Nicole, Gibbons, Henry, Currie, Bart J., Wagner, David, Keim, Paul and Tuanyok, Apichai (2015). Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates. PLoS One,10(10 - Article No. e140274).

Document type: Journal Article
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IRMA ID 10444xPUB21
Title Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates
Author Spring-Pearson, Senanu M.
Stone, Joshua K.
Doyle, Adina
Allender, Christopher J.
Okinaka, Richard T.
Mayo, Mark J.
Broomall, Stacey M.
Hill, Jessica M.
Karavis, Mark A.
Hubbard, Kyle S.
Insalaco, Joseph M.
McNew, Lauren A.
Rosenzweig, C. Nicole
Gibbons, Henry
Currie, Bart J.
Wagner, David
Keim, Paul
Tuanyok, Apichai
Journal Name PLoS One
Publication Date 2015
Volume Number 10
Issue Number 10 - Article No. e140274
ISSN 1932-6203   (check CDU catalogue open catalogue search in new window)
Scopus ID 2-s2.0-84949309339
Total Pages 22
Place of Publication United States of America
Publisher Public Library of Science
HERDC Category C1 - Journal Article (DIISR)
Abstract The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is ‘open’, with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.
DOI http://dx.doi.org/10.1371/journal.pone.0140274   (check subscription with CDU E-Gateway service for CDU Staff and Students  check subscription with CDU E-Gateway in new window)
Additional Notes This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Description for Link Link to CC Attribution 4.0 License
URL https://creativecommons.org/licenses/by/4.0/au


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