Fig. 2

Global methylation pattern in all three groups. A Violin plots showing methylation levels in all three contexts. The whole genome was split into 10-kb sub-bins, and the methylation level was calculated for each context. The x-axis is labelled with the name of each sample, and the y-axis shows the methylation level. B Circos plots for methylation levels and their differences on each chromosome for the comparison groups. The chromosomes were divided into bins, and each bin’s methylation level was calculated as follows: number of reads with mCs/(number of reads with mCs + number of reads with non-mCs). Description of the circos plot from outside to inside: methylation level for Group 1, colour denotes the methylation level (%); methylation level difference between groups, and the heatmap shows the difference (%); methylation level for Group 2, colour denotes the methylation level (%) and graph legends. The upper panel is for the progeny samples, and the lower panel is for the sperm samples. C The methylation level in the functional regions (promoter, utr5, exon, intron, utr3, CGI, CGI-shore, and repeat elements). After combining the samples with biological replicates, each functional region was divided into 20-kb bins, and the methylation level of each bin was calculated. The upper panel is for the progeny samples, and the lower panel is for the sperm samples. Graph legends contain the compared group names. D Methylation level 2 kb upstream of the TSS, 2 kb downstream of the TES, and the gene body. The upper panel is for the progeny samples, and the lower panel is for the sperm samples. Abbreviations: MOS — sperm derived from the MO chimera; HybS — sperm derived from the hybrid chimera; DoS — sperm derived from the donor; MOH — progeny derived from the MO chimera; HybH — progeny derived from the hybrid chimera; and DoH — progeny derived from the donor, n = 4 biological replicates