The Impact of Recombination on dN/dS within Recently Emerged Bacterial Clones

PLoS Pathogens

Santiago Castillo-Ramírez¹  Edward J. Feil¹  Matthew T. G. Holden²  Miao He²  Simon R. Harris²  Julian Parkhill²  Stephen D. Bentley² 

[1] Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom;The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

关键词: Staphylococcus aureus;    Cloning;    Clostridium difficile;    Homologous recombination;    Comparative genomics;    Effective population size;    Molecular genetics;    Sequence alignment;   

DOI  :  10.1371/journal.ppat.1002129

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

The development of next-generation sequencing platforms is set to reveal an unprecedented level of detail on short-term molecular evolutionary processes in bacteria. Here we re-analyse genome-wide single nucleotide polymorphism (SNP) datasets for recently emerged clones of methicillin resistant Staphylococcus aureus (MRSA) and Clostridium difficile. We note a highly significant enrichment of synonymous SNPs in those genes which have been affected by recombination, i.e. those genes on mobile elements designated “non-core” (in the case of S. aureus), or those core genes which have been affected by homologous replacements (S. aureus and C. difficile). This observation suggests that the previously documented decrease in dN/dS over time in bacteria applies not only to genomes of differing levels of divergence overall, but also to horizontally acquired genes of differing levels of divergence within a single genome. We also consider the role of increased drift acting on recently emerged, highly specialised clones, and the impact of recombination on selection at linked sites. This work has implications for a wide range of genomic analyses.

【 授权许可】

CC BY