Extended Data Fig. 5. Gene classification by CpA and CpG methylation levels.

(a) Distribution of gene body methylation levels on genes classified in deciles from lower to higher methylation levels. Few genes are CpG methylated in the honeybee (only 3 top deciles). The dynamic range of CpG gene body methylation of lampreys and birds differs from the rest of vertebrates, in which a vast majority of genes are highly methylated (>50%). Boxplot centre lines are medians, box limits are quartiles 1 (Q1) and 3 (Q3), whiskers are 1.5 × interquartile range (IQR). (b) Overlap between top and bottom decile genes classified by CpA and CpG gene body methylation levels. All deciles have the same size, thus overlap % captures the relative differences between categories in a comparable manner. (c) Level of conservation of gene sets classified by CpA and CpG gene body methylation levels. If a given orthologue is present in one subset of genes in only one species it is classified as a Singleton (1), whereas if it is found in the nine vertebrate species analyzed it is classified as 9. Each orthologue is counted once per species (e.g. if lamprey has 2 species-specific paralogues of one gene, it is only counted as 1).