Fig. 5: T. grandis seed methylomes.

a Sampled seeds for methylome profiling. Pictures show the outer side and inner side (through longitudinal section) of the seeds. b Methylation levels of exon, intron and gene flanking regions in seeds. c Methylation levels at three cytosine contexts on exonic region of genes. Genes are categorized into 20 groups based on ordered expression levels. For each group, the median value of gene expression and the average methylation level across all exonic regions of genes are recorded. d Methylation levels of intact LTR-RTs in the T. grandis genome. e GO terms enriched in genes overlapping with demethylation valleys shared by seeds of all three developmental stages. GO terms with adjusted P value < 0.05 (two-sided Fisher’s exact test with Benjamini–Hochberg correction) are plotted and sizes of GO terms in the word cloud figure correlate with their statistical significance. f View of methylation levels of selected genes overlapping with demethylation valleys. CES cellulose synthase, PE pectinesterase. g Comparison of mCG and mCHG methylation levels in different genomic regions of seeds at three stages. Source data are provided as a Source Data file.