Fig. 2

The DMR analysis between Hainan black goats and hybrid goats. A The outermost layer and innermost layers of the circle depict DNA methylation levels for the CG content in hybrid goats and Hainan black goats, respectively. The middle layer represents differences in DNA methylation levels between the two goat species. Each bin in the circos figure was 6,553,600bp. Dark blue bars indicate significantly lower (p < 0.05) DNA methylation levels in hybrid goats compared to Hainan black goats, while red bars signify significantly higher (p < 0.05) DNA methylation levels. B The outer and the inner layers distinguish between hyper and hypo DMR, while the two middle layers show the density of TE and genes. The small red, blue, and purple circles represent CG, CHG, and CHH contexts, respectively. The position of these circles relative to the center indicated the magnitude of the difference in methylation levels (diff.methylation) within DMRs. The size of the circles corresponds to the extent of the difference (areaStat) within DMRs. C Distribution of genes within DMRs across various genomic functional regions. D Comparison of gene functional regions between hyper and hypo DMRs