Chlamydia trachomatis genomes from rectal samples: description of new clade comprising ompA-genotype L4 from Argentina

Supplementary material for 'Chlamydia trachomatis genomes from rectal samples: description of new clade comprising ompA-genotype L4 from Argentina', as described in Microbial Genomics.Figure S1. Phylogeny of LGV strains without adjusting for recombination, including duplicate experiments. Duplicate experiments (n=8, to the right of the phylogeny, paired colours) show the robustness of the SureSelect method. Names of genomes from this publication are coloured in the phylogeny in light blue from Argentina and in dark blue from Finland. Names in green are those with identical duplicates (“-dup”). Scale bar refers to a phylogenetic distance of 0.00008 nucleotide substitutions per site.Figure S2. Recombination-adjusted phylogeny of LGV strains from Argentina, Finland and from previous publications showing identified recombinations. Right of the phylogeny the tracks of identified recombination are shown, with red indicating presence in multiple genomes and blue in single genomes. Above the recombination tracks are the coding sequences of strain L2b/UCH2 (AM884177) and below the tracks, peaks of recombination events. Loci affected (named from AM884177 annotation) are indicated, with those affecting in the Argentinian ompA-genotype L4 clade indicated in pale blue (the latter three only in the 10 strains in the tightly related clade). Newly sequenced isolates are shown in the phylogeny with labels in dark blue (Finland) and pale blue (Argentina). pmp=polymorphic membrane protein, inc=inclusion membrane protein, PZ=plasticity zone.Figure S3. Plasmid phylogenies. A: Phylogeny of LGV plasmids. Rooted on L3/404. Plasmids from the ompA-genotype L4 clade are indicated in boxes. B: Phylogeny of UG plasmids. Rooted on the long branch between T1 and T2 according to UG genomes. Bootstrap values are from 1000 bootstraps.Table S1. Description of samples included in the study.Suppl File 1: Whole genome alignment of LGV genomes.Suppl File 2: Whole genome alignment of UG strain and E/Bour reference.