Fig. 3

DNA methylation changes induced by interspecific hybridization were largely maintained during allotetraploid evolution. a CG (left), CHG (middle), and CHH (right) methylation changes between A2D5 hybrid and the parents (G. arboreum and G. raimondii) in gene regions. b Clustering analysis of differentially methylated regions (DMRs) between A2D5 interspecific hybrid and the parents, which were present among seven allotetraploids including two domesticated cottons. Each row indicates one DMR. Species names were abbreviated as in Fig. 1a. Black boxes indicate conserved DMRs that showed the same trend of DNA methylation changes in allotetraploids as in the A2D5 hybrid relative to progenitor-like diploid species (G. arboreum and G. raimondii). c Fraction of conserved CG, CHG, and CHH hyper or hypo DMRs in one allotetraploid (blue) or all allotetraploids (orange) shown in b. Absolute values of methylation change threshold for conserved DMRs were 0.4 for CG and CHG DMRs and 0.1 for CHH DMRs