Fig. 5

FENGC results for EMO1. (A) Genic region of EMO1. The target region is indicated by brown rectangle (target ID: AT1G27565-1 in Additional file 1: Table S1). An anaerobic-responsive element (ARE) is indicated by green brick. The transcription start site (TSS) is indicated by arrow. (B) Expression levels of EMO1 in each condition. Lowercase letters indicate significant differences between samples (FDR < 0.05 in DESeq2). (C) Average CG, CHG or CHH methylation levels in cytosines within the target region. The relative position of ARE and TSS shown in (A) are indicated by green brick and arrow, respectively. The significant differences of CG methylation level between samples in the target region are shown, in which the first CG site is omitted. One-way ANOVA with post-hoc Tukey HSD test; *, p < 0.05; ***, p < 0.001. Black arrows indicate DmCs of FER vs GER detected in WGBS using the threshold of methylation difference > 0.2 and FDR < 0.01. (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). (E) Heatmaps showing the cytosine methylation in single molecules. The heatmap panels and color legend are the same as that in Fig. 3E. Reads were hierarchically clustered using Euclidean distance based on CG methylation. The percentages of reads without methylated CG sites and reads with at least 9 consecutive unmethylated CG sites at the 3’ end are shown on the left and right side of the CG panel, respectively. One-way ANOVA with post-hoc Tukey HSD test was performed for pairwise comparisons. For percentages of reads without methylated CG sites, FER vs GER, p < 0.05; GER vs GCR, p < 0.001; FER vs FCR, p < 0.01. For percentages of reads with at least 9 consecutive unmethylated CG sites at the 3’ end, FCR vs GCR, p < 0.01; GER vs GCR, p < 0.01