Fig. 3
FENGC results for PDF1.1. (A) Genic region of PDF1.1. The target region is indicated by brown rectangle (target ID: AT1G75830-1 in Additional file 1: Table S1). A MeJA-responsive element is indicated by green brick. The transcription start site is indicated by the arrow. (B) Expression levels of PDF1.1 in each condition. Lowercase letters indicate significant differences between samples (FDR < 0.05 in DESeq2). (C) Average CG, CHG or CHH methylation levels over all sequenced molecules of the target region. The relative position of MeJA-responsive element shown in (A) is indicated by green brick. The significant differences of methylation levels between samples for CHG and CHH sites in the target region are shown. One-way ANOVA with post-hoc Tukey HSD test; *, p < 0.05; **, p < 0.01; ***, p < 0.001. Black arrows indicate DmCs detected in WGBS using the threshold of methylation difference > 0.2 and FDR < 0.01. Arrows of solid line and dot line indicate DmCs of GER vs. GCR and FER vs. GER, respectively. (D) Distribution of proportion of methylated CG, CHG or CHH sites per molecule in filtered full-length HiFi reads aligned to the target region. The significant differences of methylation proportion are shown (Kruskal-Wallis test; *, p < 0.05; **, p < 0.01; ***, p < 0.001). (E) Heatmaps showing the cytosine methylation in single molecules. Reads from the four biological replicates (Additional file 4: Table S4) were combined to generate heatmaps for each sample. If the number of combined reads exceeded 1,000, 1,000 reads were randomly selected and plotted. The three heatmap panels show the patterns of methylation at CG, CHG, and CHH sites (vertical white lines) as indicated at bottom along the same DNA molecule in each row. The color legend is the same as that in Fig. 2E. Reads were hierarchically clustered using Kendall’s Tau based on CG methylation. The relative position of MeJA-responsive element shown in (A) is indicated by green brick. A footprint (blue ovals) with consecutive protection against methylation of the first 2 CG sites in the area flanking the MeJA-responsive element is present in 8.4%, 18.0%, 39.4% and 44.0% molecules in GCR, FCR, GER and FER, respectively. One-way ANOVA with post-hoc Tukey HSD test was performed for pairwise comparisons of percentage of reads with this footprint. FCR vs. GCR, p < 0.05; GER vs. GCR, p < 0.001; FER vs. FCR, p < 0.001