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Fig. 2 | Genome Biology

Fig. 2

From: DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis

Fig. 2

Effector-triggered immune responsive genes were hyperactivated in weakly primed ddm1 plants. A Heatmaps of gene expression in Col-0 and ddm1 plants before (0 dpi; mock and BAsub) and after (1 dpi; mockDC and BAsubDC) DC inoculation. For Col-0 and ddm1 columns, log2 fold change (FC) against Col-0 mock samples were plotted. For ddm1/Col-0 columns, log2 fold change in ddm1 plants against Col-0 under four different conditions were plotted. B Heatmaps of gene expression changes after inoculation of avirulent (avrRpt2 and avrRpm1) or virulent (DC) pathogens. Log2 fold change (FC) against mock control at each time point was plotted. C Venn diagram of hyperactivated genes in ddm1 (vs. Col-0; ddm1 hyper), hyperactivated genes after avirulent pathogen inoculation (avrRpt2 or avrRpm1 vs. DC; ETI hyper), and upregulated genes in met1 (vs. Col-0; met1 up). D Observed to expected ratio of the number of overlaps between ETI hyper genes and other gene groups in C. ddm1 basal up indicates basally upregulated genes in ddm1 (vs. Col-0) under mock condition. E Venn diagram of suppressed genes in ddm1 (vs. Col-0; ddm1 sup), suppressed genes after avirulent pathogen inoculation (avrRpt2 or avrRpm1 vs. DC; ETI sup), and downregulated genes in met1 (vs. Col-0; met1 down). F Observed to expected ratio of the number of overlaps between ETI sup genes and other gene groups in E. ddm1 basal down indicates basally downregulated genes in ddm1 (vs. Col-0) under mock condition. D, F p-values by Fisher’s exact test

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