PMC:3091639 / 17543-19309 JSONTXT

{"project":"2_test","denotations":[{"id":"20646324-19749045-10032185","span":{"begin":75,"end":77},"obj":"19749045"},{"id":"20646324-9202459-10032186","span":{"begin":117,"end":119},"obj":"9202459"},{"id":"20646324-16766509-10032187","span":{"begin":370,"end":372},"obj":"16766509"},{"id":"20646324-12682364-10032188","span":{"begin":414,"end":416},"obj":"12682364"},{"id":"20646324-10684935-10032189","span":{"begin":455,"end":457},"obj":"10684935"},{"id":"20646324-16177312-10032190","span":{"begin":532,"end":534},"obj":"16177312"},{"id":"20646324-19460133-10032191","span":{"begin":540,"end":542},"obj":"19460133"},{"id":"20646324-19460133-10032192","span":{"begin":548,"end":550},"obj":"19460133"},{"id":"20646324-2836808-10032193","span":{"begin":560,"end":562},"obj":"2836808"}],"text":"Extrachromosomal plasmid sequences pCpnKo from C. pneumoniae koala LPCoLN [24], pCpnE1 from C. pneumoniae horse N16 [34], pCpA1 from C. psittaci avian N352 (Lusher ME, Gregory J, Storey CC, Richmond SJ: Analysis of the complete nucleotide sequence of the plasmid pCpA1 isolated from an avian strain of Chlamydia psittaci, Submitted), pCfe1 from C. felis feline Fe/C-56 [35], pCpGP1 from C. caviae guinea pig GPIC [36], pMoPn from C. muridarum mouse Nigg [25], and pCTA, pJALI, pSW2 and pLVG440 from C. trachomatis human serovars A [37], B [38], E [38] and L1 [39], respectively, were compared for their overall synteny and relationship (Additional file 9). These plasmids each contain eight major open reading frames (ORFs – potentially encode a protein) designated ORF1-8. Although the plasmid sequences vary in size (7169-7966 bp), alignment of their amino acid sequences revealed a high degree of similarity and large conserved regions (Additional files 9). The pCpnKo and pCpnE1 plasmid sequences share 96.2% identity and are more closely related to pCpA1 (81.3 and 78.9% identity), pCpGP1 (81.6 and 79.1% identity) and pCfe1 (77.5 and 75.1% identity) than with pMoPn (69.5 and 67.7% identity), pCTA, pJALI, pSW2 and pLVG440 (63.9-69.5% identity) (Additional file 10). Overall, there were approximately 30 indels among the species; three of the longest indels were identified in ORF1 of pCpnE1 (deletion), pCfe1 (insertion) and pSW2 (deletion). A phylogenetic tree was inferred from multiple sequence alignment of the amino acid sequence (Figure 2). Three main branches (supported with a high bootstrap value) were evident: (1) C. pneumoniae LPCoLN and N16; (2) C. psittaci N352, C. felis Fe/C-56 and C. caviae GPIC; (3) C. muridarum and C. trachomatis isolates."}