Raw data for papper titled "Transgenerational accumulation of methylome changes discovered in commercially reared honey bee (Apis mellifera) queens".
Whether a female honey bee (Apis mellifera) develops into a worker or a queen depends on her nutrition during development, which changes the epigenome to alter the developmental trajectory. Beekeepers typically exploit this developmental plasticity to produce queen bees by transplanting worker larvae into queen cells to be reared as queens, thus redirecting a worker developmental pathway to a queen developmental pathway. We studied the consequences of this manipulation for methylome over four generations. Over four generations the methylomes of lines of queens reared from eggs and worker larvae diverged, accumulating increasing differences in exons of genes related to caste differentiation, growth and immunity. We discuss the consequences of these cryptic changes to the honey bee epigenome for the health and viability of honey bee stocks. Supplemental_Figures: Figure S1. Venn diagram of the numbers of DMGs comparing L1 with E (A), and L2 with E (B) in generations G1 - G4. The letter N below indicates the number of common DMGs in generations Figure S2. Numbers of DMGs comparing GnE with G1E, GnL1 with G1L1, and GnL2 with G1L2 (n = 2, 3, or 4). Figure S3. Venn diagram of the numbers of DMGs comparing GnE with G1E (A), GnL1 with G1L1 (B), and GnL2 with G1L2 (C) (n = 2, 3, or 4). The letter N below indicates the number of common DMGs in generations. Table S1 Raw data quality control statistics Table S2 Reads and reference genome alignment results Table S3 Pearson correlation coefficient among biological replicates of each group Table S4 List of differentially methylated genes comparing L1 and L2 queens with E queens in each generation Table S5 List of differentially methylated genes comparing queens of each rearing type across successive generations Table S6 List of DMGs involved in key caste differentiation processes (body development, immunity and reproduction / longevity) differentially methylated between different rearing types with each generation of rearing. Table S7 List of 106 genes ID and the ratio of methylation levels for each comparison (within a generation, L1 with E or L2 with E) Table S8 The methylation level of the 40 genes relate to caste differentiation, body development or metabolism in each group Table S9 Raw methylation level data at the site on exon in genes S6k1 and Cat Table S10 Comparison of DEGs with those in other related articles