Fig. 5

Demethylation of COL2D during cotton domestication. a Overlap of hyper DMRs (cGh-wGh or cGb-wGb, upper panel) or hypo DMRs (cGh-wGh or cGb-wGb, lower panel) in G. hirsutum and G. barbadense. b Gene Ontology (GO) enrichment of the genes overlapped with shared DMRs between wild and cultivated cottons. c Phylogenetic tree of CONSTANS-like genes in Arabidopsis and cotton. Gene IDs for each cotton CONSTANS-like gene are shown in Additional file 9: Table S8. d Relative expression levels (R.E.L. to GhUBQ10) of GhCOL2 and GhFT in diurnal rhythms. Black and white boxes, respectively, indicate dark (16 h) and light (8 h) cycles. e During allotetraploid cotton domestication, reduced CG methylation levels correlated with increased expression levels in the COL2D locus, but COL2A was heavily methylated and silenced. Abbreviations are the same as in Fig. 1a. RPKM reads per kilobases per million. f DNA methylation levels in the boxed region of COL2D in e (D03: 32225460-32225724) (y-axis) and relative expression levels of COL2D in nine wild and nine cultivated cotton accessions. g R.E.L. (to GhUBQ10) of FT in five wild and five cultivated G. hirsutum and G. barbadense lines