Efficient inference of recombination hot regions in bacterial genomes.

ABSTRACT: In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of "hotspots" of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here, we focus in particular on identifying "hot regions" of the genome where DNA is transferred frequently between isolates. We present a computationally efficient algorithm based on the recently developed "chromosome painting" algorithm, which characterizes patterns of haplotype sharing across a genome. We compare the average genome wide painting, which principally reflects clonal descent, with the painting for each site wh

SUBMITTER: Yahara K 

PROVIDER: S-EPMC4032127 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature