Figure 4

The average Codon Adaptation index and the cumulative GC profile for TVLF. A. The average Codon Adaptation Index (CAI) for each TvLF gene in the five T. vaginalis strains investigated. Green bars represent CAI calculated using the T. vaginalis codon usage data, and the red bars using firmicute codon usage data. Firmicute codon bias based CAI is significantly higher than T. vaginalis codon bias based CAI in all strains (p ≤ 0.0001). Furthermore, CAI calculated for the reference gene-set using firmicute codon bias is significantly lower than CAI calculated using T. vaginalis codon bias data (0.01 < P ≤ 0.05). A pooled, two sample t-test was used to determine significance. Error bars represent standard errors of the mean. B1. Negative z’ curve (cumulative GC profile) for TvLF T. vaginalis G3. Segmentation points are marked with green squares, and the positions of the bacteria-like genes are indicated with blue rings. Segmentation point 3 (segmentation strength 91.69) coincides with the beginning of the first LGT (the first P. harei-like gene, TVAG_243570). B2. The GC content distribution along the TvLF, using a 1000 bp sliding window.