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Infection and Immunity, January 2006, p. 578-585, Vol. 74, No. 1
0019-9567/06/$08.00+0     doi:10.1128/IAI.74.1.578-585.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

The ompA Gene in Chlamydia trachomatis Differs in Phylogeny and Rate of Evolution from Other Regions of the Genome

Brian W. Brunelle{dagger} and George F. Sensabaugh*

Graduate Group in Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, California 94720

Received 3 June 2005/ Returned for modification 25 August 2005/ Accepted 24 October 2005

Strains of Chlamydia trachomatis are classified into serovars based on nucleotide sequence differences in ompA, the gene that encodes the major outer membrane protein. Phylogenetic characterization of strains based on ompA, however, results in serovar groupings that are inconsistent with the distinguishing features of C. trachomatis pathobiology, e.g., tissue tropisms and disease presentation. We have compared nucleotide sequences at multiple sites distributed around the chlamydial genome from 18 strains representing 16 serovars; sampled regions included genes encoding housekeeping enzymes (totaling 2,073 bp), intergenic noncoding segments (1,612 bp), and a gene encoding a second outer membrane protein (porB; 1,023 bp), with the ompA sequence (1,194 bp) used for reference. These comparative analyses revealed substantial variation in nucleotide substitution patterns among the sampled regions, with average pairwise sequence differences ranging from 0.15% for the housekeeping genes to 12.1% for ompA. Phylogenetic characterization of the sampled genomic sequences yielded a strongly supported tree that divides the strains into groupings consistent with C. trachomatis biology and which has a topology quite distinct from the ompA tree. This phylogenetic incongruity can be accounted for by recombination of the ompA gene between different genomic backgrounds. We found, however, no evidence of recombination within or between any of the sampled regions around the C. trachomatis genome apart from ompA. Parallel analysis of published sequence data on four members of the pmp gene family are consistent with the phylogenetic analyses reported here.

* Corresponding author. Mailing address: Division of Infectious Diseases, School of Public Health, 140 Earl Warren Hall, University of California, Berkeley, CA 94720. Phone: (510) 642-1271. Fax: (510) 642-6350. E-mail: sensaba{at}berkeley.edu.

Editor: A. D. O'Brien

{dagger} Present address: Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010.

Infection and Immunity, January 2006, p. 578-585, Vol. 74, No. 1
0019-9567/06/$08.00+0     doi:10.1128/IAI.74.1.578-585.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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