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Figures

- Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain

	Figure 1 Phylogenetic relationships within C. trachomatis. (A) Comparison of tree topologies produced by maximum likelihood analyses of plasmid (right) and full genome (left) sequences. Colours differentiate serotypes, as shown in the key. Branch lengths represent substitutions per site (see scale bar). Breaks in branches are equivalent to 0.4 substitutions per site. Numbers on nodes of plasmid tree represent numbers of SNPs occurring on that branch. Letters a-c indicate clades that are shown in more detail in B-D. (B-D) Detailed views of changes within clades a, b and c. Numbers on nodes represent numbers of SNPs occurring on that branch. Red stars represent deletions and blue stars represent insertions, with numbers inside the stars showing their length in bp. (Click image to enlarge)
	Figure 2 Schematic of the location of SNPs and indels within the chlamydial plasmids. The strain represented on the outer circle is plasmid pCTA from strain A/HAR-13. The positions of the CDSs are shown, with all CDSs transcribed in a clockwise direction except CDS2. The concentric circles represent (outer to inner): pLGV440, pUCH-1, pL2, pCTB, pJALI, pCHL1, pSW2, pSW3, pSW4, pSW5. The red lines indicate synonymous SNPs, the blue lines non-synonymous SNPs and the grey lines intergenic SNPs. The green bars are bases deleted in that plasmid, and the orange bars are regions of insertion/duplication. (Click image to enlarge)
	Figure 3 Comparison of plasmids pSW2 (inner circle) and pSW3 (outer circle). pSW2 carries a 377 bp deletion in CDS1 (coloured brown for pseudogene) and a 44 bp duplication immediately upstream of CDS3 (shown in red). CDS2 is transcribed in the opposite direction to the other CDSs and is shaded grey. The set of 22 bp repeats upstream of CDS1 form the putative origin of replication. (Click image to enlarge)
	Figure 4 Plasmid copy number in C. trachomatis. Quadruplicate samples of chromosomal DNA purified from EBs were analysed by qPCR to determine the plasmid/genome ratios (P/G). (Click image to enlarge)

 

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