Fig. 3
From: Heterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish
Incomplete dosage compensation regulated by DNA methylation levels. A DNA methylation levels of different gene elements in the subgenome of the two triploids and the inbred parents. Each region was divided into twenty bins based on total lengths. B Assessments of dosage compensation based on the different in silico values of homoeolog expression of the two triploids compared with those of their inbred parents. The actual values of two homoeolog expression in the triploids are marked as “ × 1.” Duplicated values of two homoeolog expression are marked as “ × 2.” Fourfold values of two homoeolog expression are marked as “ × 4.” C Differentially methylated regions (DMRs) in the two triploids and their inbred parents. D The distribution of differentially methylated genes (DMGs), for which the DMRs were located in the region of “Up in 2 k.” Crimson and dark blue represent higher methylation levels in the former comparison, while light red and light blue represent higher methylation levels in the latter comparison. The symbol “*” represents unequal numbers of gene copies between subgenomes R and C, while the symbol “**” represents equal numbers. E The potential homoeologous recombinant genes (HRGs), led by the exchange of subgenomes R and C, were predicted by the decrease of the difference in the methylation ratio between two homoeologs in both the triploids in comparison to the inbred parents. F Recombination events between the 2nRR and 2nCC subgenomes were observed in HRGs of 3nR2C and 3nRC2 based on whole-genome resequencing data. Red solid line represents in silico values of the ratio of 2nRR vs. 2nCC (log10(2) = 0.30103 in 3nR2C, log10(0.5) = − 0.30103 in 3nRC2), which were calculated based on the gene copy number of 2nRR and 2nCC in each homoeologous gene pair of the two triploids. Green dashed line represents the values of the significant ratio of 2nRR vs. 2nCC (log10(1) = 0 and log10(4) = 0.60206 in 3nR2C; log10(0.25) = − 0.60206 and log10(1) = 0 in 3nRC2), which were calculated based on the gene copy number of 2nRR and 2nCC in each homoeologous gene pair of the two triploids. Dots represent the values of the ratio of 2nRR vs. 2nCC (log10(x)), which were obtained from the read number (the average number in a 1 kb region) of 2nRR and 2nCC in each homoeologous gene pair of the two triploids. The blue solid line is obtained from the treatment of values (black dots) with method “loess” in ggplot2. Black dots are distributed between the two green lines, while the red dots (51 in 3nR2C and 50 in 3nRC2) are allocated outside of the two green lines