Reduced selection leads to accelerated gene loss in Shigella

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Abstract
Background: Obligate pathogenic bacteria lose more genes relative to facultative pathogens, which, in turn, lose more genes than free-living bacteria. It was suggested that the increased gene loss in obligate pathogens may be due to a reduction in the effectiveness of purifying selection. Less attention has been given to the causes of increased gene loss in facultative pathogens. Results: We examined in detail the rate of gene loss in two groups of facultative pathogenic bacteria: pathogenic Escherichia coli, and Shigella. We show that Shigella strains are losing genes at an accelerated rate relative to pathogenic E. coli. We demonstrate that a genome-wide reduction in the effectiveness of selection contributes to the observed increase in the rate of gene loss in Shigella. Conclusion: When compared with their closely related pathogenic E. coli relatives, the more niche-limited Shigella strains appear to be losing genes at a significantly accelerated rate. A genome-wide reduction in the effectiveness of purifying selection plays a role in creating this observed difference. Our results demonstrate that differences in the effectiveness of selection contribute to differences in rate of gene loss in facultative pathogenic bacteria. We discuss how the lifestyle and pathogenicity of Shigella may alter the effectiveness of selection, thus influencing the rate of gene loss.