Fig. 3

PCA biplots and violin plots showing DNA methylation patterns affected by diets. a Three PCA biplots show the first and second PCA components of DNA methylation rates for liver, gonads and G&L (gonads and liver) datasets. The areas of three diet groups (L1: red, L2: green, L3: blue) and two tissue types (liver: turquoise, gonads: red) are outlined with the ellipses estimated by the Khachiyan algorithm. b Violin plots show the regional distributions of methylation rates for gonads and liver datasets. Twelve PCA biplots on the right show the first and second PCA components of DNA methylation rates for c six different genomic regions (exon, intron, three promoter regions: P250, P1K and P5K, and flanking regions) and d six regions around TSS (three upstream promoter regions and three downstream exon regions from TSS). The areas of three diet groups (L1: red, L2: green, L3: blue) are outlined with the ellipses estimated by the Khachiyan algorithm