Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-11-18

AUTHORS

Talima Pearson, Philip Giffard, Stephen Beckstrom-Sternberg, Raymond Auerbach, Heidie Hornstra, Apichai Tuanyok, Erin P Price, Mindy B Glass, Benjamin Leadem, James S Beckstrom-Sternberg, Gerard J Allan, Jeffrey T Foster, David M Wagner, Richard T Okinaka, Siew Hoon Sim, Ofori Pearson, Zaining Wu, Jean Chang, Rajinder Kaul, Alex R Hoffmaster, Thomas S Brettin, Richard A Robison, Mark Mayo, Jay E Gee, Patrick Tan, Bart J Currie, Paul Keim

ABSTRACT

BACKGROUND: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. RESULTS: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. CONCLUSION: We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer. More... »

PAGES

78-78

References to SciGraph publications

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  • Journal

    TITLE

    BMC Biology

    ISSUE

    1

    VOLUME

    7

    Author Affiliations

  • Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA
  • Menzies School of Health Research, Charles Darwin University, Darwin, Australia
  • Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
  • Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
  • Bacterial Zoonoses Branch, Division of Foodborne, Bacterial, and Mycotic Diseases, National Center for Zoonotic, Vector-Borne, and Enteric Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
  • Northern Arizona University, Department of Biological Sciences, Environmental Genetics & Genomics Facility, Flagstaff, Arizona, USA
  • Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
  • Defense Medical and Environmental Research Institute, Singapore, Republic of Singapore
  • US Geological Survey, Denver Federal Center, MS 939 Denver, Colorado, USA
  • University of Washington Genome Center and Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
  • DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
  • Department of Microbiology & Molecular Biology, Brigham Young University, Provo, UT, USA
  • Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia
  • Genome Institute of Singapore, Singapore, Republic of Singapore
  • Northern Territory Clinical School, Royal Darwin Hospital, Darwin, Australia
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1741-7007-7-78

    DOI

    http://dx.doi.org/10.1186/1741-7007-7-78

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1049030306

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/19922616


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