Fig. 3

WGBS revealed that ammonium-sulfate assimilates induced the upregulation of DNA methylation level. a PCA demonstrated intra-group reproducibility and inter-group variability for T1 and T3. b Profiling analysis divided the region into 20 bins, and the methylation level in each bin reflected the trend of methylation level in the genome region. c Mean methylation levels of CG, CHG, and CHH type sites in exon, intron, UTR, and intergenic gene regions for each sample, with the horizontal coordinate being the genomic element type and the vertical coordinate indicating the methylation level, and the colors (red, green, and blue) indicated the mean methylation levels of the three types of sites. d Violin plots showed the numerical distribution of CpG, CHG, and CHH methylation levels for T1 and T3, with the vertical coordinate indicating the methylation level, and the width of each violin represented the number of points that were at that methylation level. e The Venn showed the distribution of novel DMRs of T3 and the number in CpG, CHG, and CHH types. f The location of the novel DMRs of T3 in chromosome fragment and its gene function. g FoldChange of the genes that were associated with the novel DMRs in T3 relative to T1. h Growth comparison for the mutants and WT on MM + straw. i FPA of the mutants and WT grown on MM + straw at 28 °C for 4 days. Bars represent mean ± SEM, with n = 3/4 biological repeats; red dots resemble values from individual experiments. Student’s t-testing was conducted in (i). *significant difference to WT at two-tailed P = 0.017 (i, KO-Thgh92); **significant difference to WT at two-tailed P = 0.002 (i, KO-ThgsfR2); ***significant difference to WT at two-tailed P = 0.000 (i, KO-Thabe); ns = no statistical difference to WT at two-tailed