Fig. 2
FENGC results for CML46. (A) Genic region of CML46. The target region is indicated by brown rectangle (target ID: AT5G39670-1 in S1 Table). A MYB-like binding element is indicated by green brick. The transcription start site is indicated by arrow. (B) Expression levels of CML46 in each condition. Gene expression is indicated by average count per million mapped reads (CPM) in RNA-seq reported by Paul et al. 2021. Lowercase letters indicate significant differences between samples (FDR < 0.05 in DESeq2). (C) Average CG methylation level within the target region. The relative position of MYB-like binding element shown in (A) is indicated by green brick. The region indicated by dashed frame shows significant differences of CG methylation level between FCR and GCR (one-way ANOVA with post-hoc Tukey HSD test; *, p < 0.05). (D) Distribution of proportion of methylated CG sites per molecule in filtered, full-length HiFi reads aligned to the target region. The box indicates upper/lower quartiles and whisker indicates upper/lower adjacent values. The data points of mPPM are represented by dots. The line and “x” in the box indicate median and mean, respectively. The significant differences of methylation proportion are shown (Kruskal-Wallis test; *, p < 0.05; **, p < 0.01). (E) Heatmaps showing CG methylation of single molecules. Red indicates two or more consecutively methylated cytosines, black indicates two or more consecutively unmethylated cytosines, and gray indicates transitions between methylated and unmethylated cytosines. The reads from the four biological replicates (Additional file 4: Table S4) were combined to generate heatmaps for each sample. The relative position of MYB-like binding elements shown in (A) and (C) are indicated by green brick. The region used for the CG methylation level comparison in (C) is indicated by dashed frame. Approximately 6.9% of reads in GCR and 12% of reads in FCR containing at least two consecutively methylated CG sites in both areas flanking the MYB-like binding element are labeled by blue bricks. One-way ANOVA with post-hoc Tukey HSD test was performed for pairwise comparisons of percentage of reads with this signature. FER vs. FCR, p < 0.01