TABLE 2.

Representation of DMRs amongst the three main categories of DEGs.

	CG Gain		CG Loss		CHG Gain		CHG Loss		CHH Loss
	Gene	Promoter	Gene	Promoter	Gene	Promoter	Gene	Promoter	Gene	Promoter
Control only	0.45	0.26	0.78	0.67	0.50	0.00	0.39*	0.87	1.72	1.55*
BABA and control	0.30	0.34	0.51	1.46	0.66	0.87	0.52	1.03	1.50	1.89**
BABA only	1.01	1.24	0.68	1.15	0.61	0.92	0.98	1.12	1.64**	1.72***

Figures show the enrichment of DMRs in DEG lists (proportion of genes in the DEG list containing DMRs relative to the proportion of genes with DMRs in the whole genome). Enrichment was calculated separately for hypermethylation (gain) and hypomethylation (loss) in CG, CHG, and CHH methylation contexts in the transcribed region (Gene) and promoter region of each gene. Asterisks represent statistical significance (*P < 0.05, **P < 0.01, ***P < 0.001 by Fisher’s exact test).