Interplay of recombination and selection in the genomes of Chlamydia trachomatis

• Type of Material: Article
• Authors: Sandeep J. Joseph, Emory University; Xavier Didelot, University of Oxford; Khanjan Gandhi, Emory University; Deborah Dean, University of California; Timothy D Read, Emory University
• Language: English
• Date: 2011-05-26
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: © 2011 Joseph et al; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://www.biologydirect.com/content/6/1/28
• Title of Journal or Parent Work: Biology Direct
• ISSN: 1745-6150
• Volume: 6
• Issue: 28
• Start Page: 1
• End Page: 16
• Grant/Funding Information: This work was supported in part by Emory University faculty Development funds, grants from the National Institutes of Health, R01 AI059647 (to DD), and from the National Science Foundation/United States Department of Agriculture Microbial Genome Sequencing and Microbial Observatories Program, NSF-USDA 2009-65109-05760 NSF-USDA (to DD).
• Research Categories: Biology, Genetics; Engineering, Biomedical

Abstract

Background Chlamydia trachomatis is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published C. trachomatis genomes to assess the contribution of recombination and selection in this pathogen and to understand the major evolutionary forces acting on the genome of this bacterium. Results The conserved core genes of C. trachomatis are a large proportion of the pan-genome: we identified 836 core genes in C. trachomatis out of a range of 874-927 total genes in each genome. The ratio of recombination events compared to mutation (ρ/θ) was 0.07 based on ancestral reconstructions using the ClonalFrame tool, but recombination had a significant effect on genetic diversification (r/m = 0.71). The distance-dependent decay of linkage disequilibrium also indicated that C. trachomatis populations behaved intermediately between sexual and clonal extremes. Fifty-five genes were identified as having a history of recombination and 92 were under positive selection based on statistical tests. Twenty-three genes showed evidence of being under both positive selection and recombination, which included genes with a known role in virulence and pathogencity (e.g., ompA, pmps, tarp). Analysis of inter-clade recombination flux indicated non-uniform currents of recombination between clades, which suggests the possibility of spatial population structure in C. trachomatis infections. Conclusions C. trachomatis is the archetype of a bacterial species where recombination is relatively frequent yet gene gains by horizontal gene transfer (HGT) and losses (by deletion) are rare. Gene conversion occurs at sites across the whole C. trachomatis genome but may be more often fixed in genes that are under diversifying selection. Furthermore, genome sequencing will reveal patterns of serotype specific gene exchange and selection that will generate important research questions for understanding C. trachomatis pathogenesis.