(A) More than half of all methylated positions in S. pistillata are located in annotated introns. (B) Introns have proportionally more methylated positions (11.3%) than exons (8.6%) or intergenic regions (3.3%) even when accounting for the different amounts of CpG dinucleotides in the respective regions. (C) Distribution of methylated positions across a standardized gene model with flanking 4-kb regions. Solid lines depict transcription start site (left) and transcription termination site (right). Exons and introns in the plot have normalized lengths that correspond to their respective mean lengths in S. pistillata (from left to right: 373, 1258, 363, 1114, 302; 253, 967, 312, 1037, and 669 bp). arb. units, arbitrary units.