Fig. 3

T. vaginalis mRNAs exhibit a characteristic structural pattern, which is associated with TE variation. a Structural pattern and variation of GC content across the length of T. vaginalis mRNAs from Dataset 1. Following the exclusion of genes with unpredictable TSS and combination of genes with > 90% sequence identity (Figure S2), a total of 713 genes were included in this analysis. Genes were sliced into a series of 30 nt wide windows following a sliding window scheme. The index of a window was determined by the position of its central nucleotide relative to the start codon. The value on y axis is the mean MFE value (left) and GC percentage (right) of all sequences from the same window position and the error bar indicates the 95% confidence interval. Values of MFE and GC content for Dataset 1 and the MFE values of the permuted sequences were plotted (red, green and grey curves respectively). Independent t-tests were performed for the two MFE values (original vs. permuted) at the same window position and regions were shaded in yellow if p < 0.05, following Bonferroni Correction (α = 0.05). b-c Comparisons of mRNA folding patterns between T. vaginalis genes with different TE: b Green and magenta curves represent the top and bottom 200 genes with the highest and lowest TE values in Dataset 1, respectively; c Red and blue curves represent genes in Datasets 2 (MS evidence only) and Dataset 3 (EST evidence only), respectively. Independent t-tests were performed for the two MFE values at the same window position and regions were shaded in yellow if p < 0.05, following Bonferroni Correction (α = 0.05)