Figure 2

Cytosine modifications in introns are predominantly in the low-CpG content genes. a, plot of EHB genes (N = 514) with >90% methylation at CpG sites. The dashed line shows the bimodal distribution of bee genes with low o/e and high o/e (observed/expected) CpG ratios. The number of genes in the bimodal o/e plot is shown on the left Y-axis. The percentage of genes with >90% methylation in each region of the bimodal o/e plot is shown on the right Y-axis. b, plot of EHB genes (N = 2912) with zero percent CpG methylation. Since there are a large number of genes in all three classes with zero percent methylation, we restricted our analyses to genes with multiple motifs as follows: for CpG, there are 2912 genes with at least 10 total CpGs in the exons with 0% methylation. c, plot of EHB genes (N = 615) with >10% methylation at CHH sites in introns. d, plot of EHB genes (N = 555) with zero percent methylation at CHH sites in introns. For CHH, there are 555 genes with zero percent methylation in introns that have at least 400 total CHHs in the introns. e, plot of EHB genes (N = 245) with >10% methylation at CHG sites in introns. f, plot of EHB genes (N = 1364) with zero percent methylation at CHG sites in introns. For CHG, there are 1364 genes with zero percent methylation with at least 100 total CHGs in the introns.