Genome Sequencing and Evolution of Chlamydophila and Chlamydia Species of Animal Origin

Chlamydia psittaci is a Gram-negative obligate intracellular pathogen that causes a diversity of severe, life threatening diseases among humans and lower vertebrate species, imparting a huge economic burden on livestock and animal breeding facilities.  Both avian and mammalian species can transmit chlamydiae to humans who are an accidental dead-end host. We developed a workflow for comparative genomic analyses of 20 diverse (serotype and host specificity) C. psittaci strains, 12 of which were sequenced by the Roche/454 GS-FLX sequencer as part of this proposal. The workflow included estimating population structure using STRUCTURE, identifying core genes using ORTHOMCL, detecting genes under purifying selection using PAML for each clade, estimating effects of genetic drift by calculating genome-wide dN/dS ratios for each genome and comparing genetic drift between the clades, estimating recombination using ClonalFrame, analyzing inter-clade recombination flux, and detecting recombinant breakpoints among whole-genome alignments using a combined algorithm for estimating tree structure and hidden Markov model parameters. Human DNA contamination was removed by alignment of reads to the human genome sequence. In each case, contamination was < 1.5%. Genes were predicted for each genome using DIYA software. Predicted proteomes of the genomes were combined with those of completed Chlamydia species and clustered using the OrthoMCL pipeline. We identified 643 proteins conserved across Chlamydia and generated a list of proteins unique to each genome. We found that the clonal recombination rate was significantly higher than for Chlamydia trachomatis where we similarly analyzed 32 genomes representing diverse serotypes and genotypes.