Fig. 3

Gene body methylation is robustly maintained during honey bee development. a Kernel density plots of percent-methylation-change between averaged methylation in embryo versus indicated samples calculated for single cytosines (Single-Cs). Negative and positive numbers in the x-axis indicate greater and lower methylation in embryo and the other sample, respectively. Partial and fully differentially methylated cytosines (pDMC/fDMC) were considered if the percent-methylation-change was lower and higher than 90%, respectively. b Box plots of averaged embryonic methylation in single cytosines (left) and exons (right) derived from partially and fully differentially methylated sites between embryo and indicated samples. c, d Kernel density plots of percent-methylation-change between averaged methylation of single-Cs in embryo versus indicated samples, of cytosines derived from lowly methylated in embryo (c) or highly methylated in embryo (d). e Kernel density plots of percent-methylation-change between averaged methylation in embryo versus indicated samples calculated for single exons. Partial and fully differentially methylated exons (pDME/fDME) were annotated as in a. f Scatter plot of percent-methylation-change between embryo/D. larva and embryo/W. larva in exons. r is Pearson correlation coefficient value. g Hierarchical clustering heatmap showing average methylation in individual exons in the different biological samples. Scale bar indicates methylation level. h Kernel density plots of percent-methylation-change between averaged methylation in embryo versus indicated samples calculated for single genes. Partial and fully differentially methylated genes (pDMG/fDMG) were annotated as in a. i Scatter plot of percent-methylation-change between embryo/D. larva and embryo/W. larva in genes