DNA methylation comparison between 4-day-old queen and worker larvae of honey bee

The honey bee is a social insect that is famous for queen-worker differentiation. Numerous studies indicate that queen larvae (QL) and worker larvae (WL) have different expressed genes and proteins. DNA methylation has been found to play an important role in regulating gene expression. To further explore the roles of the methylated genes in queen-worker differentiation, we analyzed DNA methylome profiles of 4-day-old QL and WL (Apis mellifera). The results demonstrated that there were 7.2 gigabases of sequence data from six methylated DNA immunoprecipitation libraries, and provided a genome-wide DNA methylation map as well as a gene expression map for 4-day-old QL and WL. The genome coverage of every sample was 4.79. According to CpG representation, all promoters in the A. mellifera genome were classified into high CpG promoters, intermediate CpG promoters and low CpG promoters. The methylated cytosines of larvae were enriched in introns, followed by coding sequence regions, 2 K downstream of genes, 5′ untranslated regions (UTRs), 2 K upstream of genes, and 3′ UTRs. Compared with 4-day-old WL, a number of genes in QL were down-methylated that were involved in biological regulation, immune system and metabolic regulation. In addition, these DMGs were involved in many signal pathways of caste differentiation such as Mitogen-activated protein kinase (MAPK), Notch, Insulin and Wnt signaling pathways.