Fig. 1

Generic methylation patterns in plants. Genes (dark orange boxes) are CG methylated (blue dots) but can also contain non-CG methylation (green and red dots) if TEs or TE fragments (light orange boxes) are present internally. TEs are methylated in all sequence contexts, with CHH methylation more concentrated at TE ends than internal regions in some species. Other sequence features, such as direct repeats (green arrows), are also subject to DNA methylation in all sequence contexts