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

Simple item page
dc.contributor.authorSmith, Silvia Een_ZA
dc.contributor.authorShowers-Corneli, Patriceen_ZA
dc.contributor.authorDardenne, Caitlin Nen_ZA
dc.contributor.authorHarpending, Henry Hen_ZA
dc.contributor.authorMartin, Darren Pen_ZA
dc.contributor.authorBeiko, Robert Gen_ZA
dc.date.accessioned2015-12-28T06:47:42Z
dc.date.available2015-12-28T06:47:42Z
dc.date.issued2012en_ZA
dc.description.abstractThe 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.identifier.apacitationSmith, 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. <i>PLoS One</i>, http://hdl.handle.net/11427/16042en_ZA
dc.identifier.chicagocitationSmith, Silvia E, Patrice Showers-Corneli, Caitlin N Dardenne, Henry H Harpending, Darren P Martin, and Robert G Beiko "Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution." <i>PLoS One</i> (2012) http://hdl.handle.net/11427/16042en_ZA
dc.identifier.citationSmith, 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.0050070en_ZA
dc.identifier.ris TY - Journal Article AU - Smith, Silvia E AU - Showers-Corneli, Patrice AU - Dardenne, Caitlin N AU - Harpending, Henry H AU - Martin, Darren P AU - Beiko, Robert G AB - 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. DA - 2012 DB - OpenUCT DO - 10.1371/journal.pone.0050070 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2012 T1 - Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution TI - Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution UR - http://hdl.handle.net/11427/16042 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/16042
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pone.0050070
dc.identifier.vancouvercitationSmith SE, Showers-Corneli P, Dardenne CN, Harpending HH, Martin DP, Beiko RG. Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. PLoS One. 2012; http://hdl.handle.net/11427/16042.en_ZA
dc.language.isoengen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis 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.holder© 2012 Smith et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLoS Oneen_ZA
dc.source.urihttp://journals.plos.org/plosoneen_ZA
dc.subject.otherPhylogenetic analysisen_ZA
dc.subject.otherMycobacterium tuberculosisen_ZA
dc.subject.otherPhylogeneticsen_ZA
dc.subject.otherHomologous recombinationen_ZA
dc.subject.otherSequence alignmenten_ZA
dc.subject.otherDNA recombinationen_ZA
dc.subject.otherMycobacteriaen_ZA
dc.subject.otherCorynebacteriaen_ZA
dc.titleComparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolutionen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Smith_Genomic_and_Phylogenetic_Approaches_2012.pdf
Size:
915.15 KB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Journal Articles