Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting genotypes mediated by genomic inversions in bacterial cultures. We tested our method on widely used strains of Escherichia coli, and detected stable and reproducible phase variation in several invertible loci. These are shown here to be responsible for maintaining constant variation in populations grown from a single colony. Applying this tool on other bacterial strains can shed light on how pathogens adjust to hostile environments by diversifying their genomes.
Bibliographical noteFunding Information:
We would like to thank Liran Carmel and Rotem Sorek for comments on the manuscript, Amir Eden for his enlightening insight and Ilan Rosenshine for strains and advice. The work is supported by European Research Council (Starting Grant #260871) and the Israel Science Foundation (592/10).
© 2014 Goldberg et al.; licensee BioMed Central Ltd.