Fig. 4
DNA methylation changes between diploid species (G. arboreum and G. raimondii) and allotetraploid cottons. a Fraction of CG, CHG, and CHH hyper or hypo DMRs between diploid and wild allotetraploid cottons in different genomic features. Intergenic regions indicate those located between gene bodies excluding TEs. b CG methylation levels of Ga (A), Gr (D), Gh A subgenome (As), and D subgenome (Ds) in genic regions. c Log2 expression ratios (wGh/diploids) of all genes, hypermethylated genes, and hypomethylated genes. d An example of CG hypomethylated gene (Cotton_A_00760) in diploid (Ga), A2D5, and five wild allotetraploids (wGh, wGb, Gt, Gm, and Gd). RPKM reads per kilobase per million. e CG methylation patterns of DMRs between G. arboreum (Ga) and G. raimondii (Gr) (mCGA-D > 0.6) in Ga (A) and Gr (D) and in the wild allotetraploid G. hirsutum consisting of A subgenome (As) and D subgenome (Ds). Each row indicates one DMR between G. raimondii and G. arboreum. Red and black brackets indicate conserved DMRs (cDMRs, mCGAs-Ds > 0.6) and homoeologous DNA methylation changes (hDMCs, mCGAs-Ds < –0.6), respectively. f Fraction of the homoeologs with hDMCs and the homoeologs with cDMRs, respectively, showed expression bias