Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution

 

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dc.contributor.author Smith, Silvia E en_ZA
dc.contributor.author Showers-Corneli, Patrice en_ZA
dc.contributor.author Dardenne, Caitlin N en_ZA
dc.contributor.author Harpending, Henry H en_ZA
dc.contributor.author Martin, Darren P en_ZA
dc.contributor.author Beiko, Robert G en_ZA
dc.date.accessioned 2015-12-28T06:47:42Z
dc.date.available 2015-12-28T06:47:42Z
dc.date.issued 2012 en_ZA
dc.identifier.citation Smith, S. E., Showers-Corneli, P., Dardenne, C. N., Harpending, H. H., Martin, D. P., & Beiko, R. G. (2012). Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. PLoS One, 7(11), e50070. doi:10.1371/journal.pone.0050070 en_ZA
dc.identifier.uri http://hdl.handle.net/11427/16042
dc.identifier.uri http://dx.doi.org/10.1371/journal.pone.0050070
dc.description.abstract The genus Mycobacterium encompasses over one hundred named species of environmental and pathogenic organisms, including the causative agents of devastating human diseases such as tuberculosis and leprosy. The success of these human pathogens is due in part to their ability to rapidly adapt to their changing environment and host. Recombination is the fastest way for bacterial genomes to acquire genetic material, but conflicting results about the extent of recombination in the genus Mycobacterium have been reported. We examined a data set comprising 18 distinct strains from 13 named species for evidence of recombination. Genomic regions common to all strains (accounting for 10% to 22% of the full genomes of all examined species) were aligned and concatenated in the chromosomal order of one mycobacterial reference species. The concatenated sequence was screened for evidence of recombination using a variety of statistical methods, with each proposed event evaluated by comparing maximum-likelihood phylogenies of the recombinant section with the non-recombinant portion of the dataset. Incongruent phylogenies were identified by comparing the site-wise log-likelihoods of each tree using multiple tests. We also used a phylogenomic approach to identify genes that may have been acquired through horizontal transfer from non-mycobacterial sources. The most frequent associated lineages (and potential gene transfer partners) in the Mycobacterium lineage-restricted gene trees are other members of suborder Corynebacterinae, but more-distant partners were identified as well. In two examined cases of potentially frequent and habitat-directed transfer ( M. abscessus to Segniliparus and M. smegmatis to Streptomyces ), observed sequence distances were small and consistent with a hypothesis of transfer, while in a third case ( M. vanbaalenii to Streptomyces ) distances were larger. The analyses described here indicate that whereas evidence of recombination in core regions within the genus is relatively sparse, the acquisition of genes from non-mycobacterial lineages is a significant feature of mycobacterial evolution. en_ZA
dc.language.iso eng en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. en_ZA
dc.rights.uri http://creativecommons.org/licenses/by/4.0 en_ZA
dc.source PLoS One en_ZA
dc.source.uri http://journals.plos.org/plosone en_ZA
dc.subject.other Phylogenetic analysis en_ZA
dc.subject.other Mycobacterium tuberculosis en_ZA
dc.subject.other Phylogenetics en_ZA
dc.subject.other Homologous recombination en_ZA
dc.subject.other Sequence alignment en_ZA
dc.subject.other DNA recombination en_ZA
dc.subject.other Mycobacteria en_ZA
dc.subject.other Corynebacteria en_ZA
dc.title Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution en_ZA
dc.type Journal Article en_ZA
dc.rights.holder © 2012 Smith et al en_ZA
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department Institute of Infectious Disease and Molecular Medicine en_ZA
uct.type.filetype Text
uct.type.filetype Image


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This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Except where otherwise noted, this item's license is described as This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.