Phylogenetic analysis of sequenced chlamydial isolates based on whole-genome alignment. The tree was constructed using a modified UPGMA (unweighted-pair group method using average linkages) algorithm as part of the MAFFT alignment program. Strains collected from the male rectum are indicated by outlined type, and cervical isolates are indicated by standard type. The branch lengths are proportional to the genetic distances between isolates.

Numbers of substitutions per open reading frame for comparisons of strains. Each graph represents a Diffseq-generated whole-genome alignment for the strains indicated. The genes, beginning with CT001, are indicated on the x axis; the sequenced strain D/UW3 gene designations were used as a reference. The numbers of substitutions per ORF are indicated on the y axis. Strains collected from the male rectum are indicated by outlined type, and cervical isolates are indicated by standard type.

Locations of insertions or deletions in strains. The comparisons are identical to and in the same order as those shown in Fig. 2. The genes, beginning with CT001, are indicated on the x axis; the sequenced strain D/UW3 gene designations were used as a reference. The y axis indicates the lengths of the insertions (above the x axis) and deletions (below the x axis). For each graph the strain listed first has an insertion or a deletion at a given site compared to the strain listed second. For example, G/9768 has a 437-bp insertion in CT154 compared to D/UW3. Strains collected from the male rectum are indicated by outlined type, and cervical isolates are indicated by standard type.

Schematic diagram of open reading frames CT154 and CT326 in several sequenced C. trachomatis strains. The isolate designations are indicated on the left. Strains isolated from the male rectal site of infection are indicated by outlined type, and cervical isolates are indicated by standard type. The ORF examined is indicated by a dark gray arrow, and lighter gray arrows and boxes indicate flanking ORFs. The boxes with diagonal stripes indicate the locations of insertions in the genes. Putative new ORFs resulting from an insertion are indicated by open arrows. The numbers above the brackets indicate the lengths (in base pairs) of insertions based on a comparison with the D/UW3 sequence.

BLAST-based evidence for recombination in clinical C. trachomatis genome sequences. Complete genome sequences of strain Ds/2923 (A) and strain F/70 (B) were used as probes with a genome database containing sequences of D/UW3, G/9768, J/6276, E/11023, and (in panel A) F/70. The complete genome sequence of each probe was evaluated using BLAST analysis of a 1-kbp sliding window, and each window was given a score based on whether it was more similar to a clade containing serovar J, G, or D, it was more similar to a clade containing serovar E or F, or it was equally similar to all the genomes. The results for each window are plotted on the x axis beginning with ORF CT001 as defined for the D/UW3 genome (37). All ORF designations are also based on the D/UW3 genome sequence. Panel A includes ORF maps showing expanded views of three regions showing apparent recombination. In the ORF maps, a gray box or arrow indicates that the sequence is more similar to E/11023, an open box or arrow indicates that the sequence is more similar to D/UW3, and a black box or arrow indicates a region where apparent recombination events occurred. The brackets above the gene diagrams indicate the regions for which informative sites were examined and counted. The numbers above the brackets indicate the numbers of informative sites shared by the Ds/2923 and D/UW3 sequences (top line) or the Ds/2923 and E/11023 sequences (bottom line). The asterisk indicates that 1 of the 66 shared informative sites is a 308-nucleotide deletion that D/UW3 and Ds/2923 share compared to the E/11023 sequence. The identified areas in panel B are selected regions of the F/70 genome that are more similar to genomes of strains in the serovar J-serovar G-serovar D clade than to the genomes of serovar E strains.

PCR- and RFLP-based genotype analysis of variable regions in clinical isolates. The strains, dates of isolation, and sites of isolation are indicated on the left. (A) Data for serovar G isolates. (B) Data for serovars E and J. (C) Results of statistical analyses with Fisher's exact test. One asterisk indicates that the P value is <0.01, and two asterisks indicate that the P value is <0.001. Isolates indicated by bold type are the isolates whose complete genome sequences were examined. Isolates whose designations end with P were collected from patients in Lima, Peru, and isolates whose designations end with AB were collected from patients in Birmingham, AL. All other isolates were collected from patients in King County, WA, area family planning clinics. The designations beginning with CT at the top indicate the gene targets for the PCR and RFLP analysis. CT456-N and CT456-C indicate variable regions that are present at the amino and carboxy termini of CT456. The different types of boxes indicate the genotypes detected, as follows: open boxes, D/UW3 genotype; gray boxes, rectal serovar G genotype; black boxes, serovar E genotype; diagonally striped boxes, cervical serovar G genotype.