Fig. 4

Integrative analysis of methylome and transcriptome revealed expression regulation of drought response genes. (A) Methylation levels of genomic fractions (gene bodies and their upstream and downstream 2 kb regions) of different expression classes: low to high expression levels correspond to the lower, middle, and upper quartiles of FPKM, with FPKM < 1 indicating no expression (none); (B) The shared 835 genes were subjected to methylome-transcriptome association analysis; (C) Box plots of gene expression levels of all DEGs, hypermethylated and hypomethylation-DGEs. The turquoise dotplot in the middle represents gene numbers and corresponding expression levels. *** P.adj < 0.001 (ANOVA, Tukey_HSD); (D, E) Identifies the association of promoter and gene body methylation with the expression of 835 genes. C1: Hypermethylation and low expression; C2: Hypomethylation and high expression; C3: Hypermethylation and high expression; C4: Hypomethylation and low expression. Detailed gene lists are shown in supplementary data Table 4