Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA

Chlamydia pneumoniae is a widespread pathogen of humans causing pneumonia a nd bronchitis. There are many reports of an association between C.pneumonia e infection and atherosclerosis. We determined the whole genome sequence of C.pneumoniae strain J138 isolated in Japan in 1994 and compared it with th e sequence of strain CWL029 isolated in the USA before 1987. The J138 circu lar chromosome consists of 1 226 565 nt (40.7% G+C) with 1072 likely protei n-coding genes that is 3665 nt shorter than the CWL029 genome. Plasmids, ph age- or transposon-like sequences were not identified. The overall genomic organization, gene order and predicted proteomes of the two strains are ver y similar, suggesting a high level of structural and functional conservatio n between the two unrelated isolates. The most conspicuous differences in t he J138 genome relative to the CWL029 genome are the absence of five DNA se gments, ranging in size from 89 to 1649 nt, and the presence of three DNA s egments, ranging from 27 to 84 nt. The complex organization of these 'diffe rent zones' may be attributable to a unique system of recombination.