Inference of homologous recombination in bacteria using whole-genome sequences.

ABSTRACT: Bacteria and archaea reproduce clonally, but sporadically import DNA into their chromosomes from other organisms. In many of these events, the imported DNA replaces an homologous segment in the recipient genome. Here we present a new method to reconstruct the history of recombination events that affected a given sample of bacterial genomes. We introduce a mathematical model that represents both the donor and the recipient of each DNA import as an ancestor of the genomes in the sample. The model represents a simplification of the previously described coalescent with gene conversion. We implement a Monte Carlo Markov chain algorithm to perform inference under this model from sequence data alignments and show that inference is feasible for whole-genome alignments through parallelization. Usin

SUBMITTER: Didelot X 

PROVIDER: S-EPMC2998322 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature