Fig. 3

Variation in levels of DNA methylation within gene bodies across Viridiplantae. a DNA methylation at CG, CHG, and CHH sites within gene bodies can be found in the majority of species investigated. Variation of DNA methylation levels within gene bodies at all sequence contexts is high across all land plants and within major taxonomic groups. mCG levels are typically higher than mCHG, followed by mCHH. However, levels of mCG and mCHG within genes are similar in gymnosperms and ferns. Error bars represent 95% confidence intervals for species with low sequencing coverage. Cladogram was generated from Open Tree of Life [53]. b The distribution of DNA methylation within genes (all [dashed lines] and mCG-enriched/gbM [solid lines]) has diverged among taxonomic groups of Viridiplantae represented by specific species. Based on the distribution of DNA methylation, and number of mCG-enriched genes, gbM is specific to angiosperms. However, mCG-enriched genes in P. taeda share some DNA methylation characteristics to A. trichopoda. However, other characteristics associated with gbM genes remains unknown at this time for mCG-enriched genes in gymnosperms and other early diverging Viridiplantae. The yellow highlighted line represents the average from 100 random sampling of 100 gbM genes in angiosperms and was used to assess biases in numbers of mCG-enriched genes identified. NCR non-conversion rate, TSS transcriptional start site, TTS transcriptional termination site