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

Autor: Zaining Wu, Mindy B. Glass, Siew Hoon Sim, Bart J. Currie, Paul Keim, Erin P. Price, Rajinder Kaul, Mark Mayo, Apichai Tuanyok, Gerard J. Allan, Ofori Pearson, Jeffrey T. Foster, Heidie Hornstra, Jay E. Gee, Benjamin Leadem, Thomas Brettin, Talima Pearson, Stephen M. Beckstrom-Sternberg, Richard T. Okinaka, Philip M. Giffard, Patrick Tan, James S. Beckstrom-Sternberg, Alex R. Hoffmaster, Richard A. Robison, Raymond K. Auerbach, David M. Wagner, Jean Chang
Jazyk: angličtina
Rok vydání: 2009
Předmět:
DNA
Bacterial
Burkholderia pseudomallei
Gene Transfer
Horizontal
Physiology
Population
Population genetics
Sequence Homology
Plant Science
Bacterial genome size
Gene mutation
Biology
Polymorphism
Single Nucleotide
General Biochemistry
Genetics and Molecular Biology
03 medical and health sciences
Structural Biology
Phylogenetics
Research article
Humans
education
lcsh:QH301-705.5
Ecology
Evolution
Behavior and Systematics
Phylogeny
030304 developmental biology
Genetics
0303 health sciences
Genetic diversity
education.field_of_study
Molecular Epidemiology
Phylogenetic tree
030306 microbiology
Australia
Cell Biology
Sequence Analysis
DNA
15. Life on land
Genetics
Population
lcsh:Biology (General)
Genes
Bacterial
Horizontal gene transfer
General Agricultural and Biological Sciences
Genome
Bacterial
Developmental Biology
Biotechnology
Zdroj: BMC Biology, Vol 7, Iss 1, p 78 (2009)
BMC Biology
ISSN: 1741-7007
Popis: 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.
Databáze: OpenAIRE
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