Fig. 1

Evolution of DNA methylation and genome sequence during polyploidization in cotton. a Allotetraploid cotton (AADD) was formed between A-genome species like G. arboreum (Ga) and D-genome species like G. raimondii (Gr), giving rise to five allotetraploid species: wild G. hirsutum (wGh), wild G. barbadense (wGb), G. tomentosum (Gt), G. darwinii (Gd), and G. mustelinum (Gm). Wild Gh and Gb are domesticated into cultivated G. hirsutum (cGh) and G. barbadense (cGb), respectively. b The number of differentially methylated cytosines in CG context (DmCG) in each pairwise comparison between different cotton species as shown in a. A2D5 is an interspecific hybrid between Ga (A2) and Gr (D5). Blue, green, black, and yellow brackets indicate comparisons of wild vs. wild, cultivated vs. wild allotetraploids, diploid vs. allotetraploid, and diploid parents vs. interspecific hybrid, respectively. c Phylogenetic tree was reconstructed based on genome-wide mCG divergent levels among cotton species. d, e Distribution of synonymous substitution values (Ks) (left) and gene-body DmCG percentages (right) of 6781 methylated orthologous genes (d) and 4063 unmethylated orthologous genes (e). As, Ds A subgenome and D subgenome in cultivated G. hirsutum, A G. arboreum, D G. raimondii. Peak values are indicated by arrows. The rate of methylation changes in each gene pair was estimated as the number of DmCG divided by the total number of CG in the gene body