DNA methylation differences in homoeologous genes.

<p>(A) Pairwise plots of CG (left), CHG (middle), and CHH (right) methylation levels (Y-axis, D homologs; X-axis, A homoeologs) in the gene body for homoeologous genes. Blue and red dots indicate the expression level of an A homoeolog that is lower and higher than that of the corresponding D homoeolog, respectively. Spearman correlation coefficient (r) is shown. Fold-changes of expression (>2-fold) between A and D homoeologs were used as cut-off values. (B) Number of homoeologous genes that were differentially methylated in the gene body and showed expression differences (A < D, blue; A > D, red). The levels of CG (>0.4), CHG (>0.4), and CHH (>0.1) methylation difference and fold-changes of expression (>2-fold) between A and D homoeologs were used as cut-off values. (C) An example of hypermethylation in the gene body correlating with repression of the A-homoeolog. Colors indicate CG (green). CHG (blue), and CHH (red) methylation, and gene expression (black).