FIG 3.

Map of tprK donor sites flanking the tprD locus. Variable region sequences were blastn aligned against a 12.5-kb locus that contained putative tprK donor sites based on manual review. (A) The usage of all 53 donor sites across the tprD locus by variable region is depicted based on the sum of within-sample percentages across all 41 samples. The nucleotide numbering of the tprD locus is based on the reference strain SS14 (NC_021508.1). (B) Zoomed-in depiction of the locus immediately downstream of tprD containing tprK donor sites. Donor sites are in the same orientation as the tprD locus. The light-brown sites include 45 of the 47 donor sites reported previously by Centurion et al. (14). The bottom donor sites include 51 of the 53 donor sites found in this study and are colored based on their associated variable region. (C) Length in nucleotides of the 53 donor sites identified from the analysis of tprK deep sequencing data from 41 clinical T. pallidum subsp. pallidum strains. The usage, represented as a sum percentage, as well as the variable region of each donor site is also depicted. The GFF file of the donor site locus is included as Data Set S3.