Additional file 1: of Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation

Figure S1. Comparison of fold coverage at methylated CG sites in thelytokous and fertilized embryos. Both samples exhibit a median coverage of 5 reads, thus our comparison of differential methylation was restricted to CG sites with at least 5 reads in both samples. Figure S2. Direct sequencing of bisulfite PCR products of Stoned B (GB17165) from colony 2 and 3 fertilized and thelytokous embryos. Red ovals indicated methylated cytosines, blue squares indicate SNPs. Figure S3. Direct sequencing of bisulfite PCR products of Sap30 (GB18386) from colony 2 and 3 fertilized and thelytokous embryos. Red ovals indicate methylated cytosines, open circles indicate total number of CG sites in the region, and dashed lines indicate incomplete sequence reads. Also shown is the methylation patterns in fertilized and thelytokous embryos from whole genome bisulfite sequencing of Colony 1. Asterisk indicates CG sites that are hypermethylated in fertilized embryos, dagger indicates CG sites hypermethylated in thelyokous embryos. Table S1. Non-CG methylation in Fertilised and Thelytokous embryos and comparison to Apis mellifera Capensis SNPs. Table S2. Primers used in bisulfite nested PCRs of Stan (Fig. 6), Stoned B (Additional file 1: Figure S2), Sap30 (Additional file 1: Figure S3, Syd and Pcl. (PPTX 607 kb)