Potential interaction between DNA demethylases and RdDM in Arabidopsis response to Fo . (A) Overlap of differentially expressed genes between rdd and the RdDM mutants. The number in blue (133) represents genes differentially expressed in both the rdd mutant and the two RdDM mutants. Note that the total numbers of differentially expressed genes for the three mutants (1,397, 1,169, and 347 for nrpd1, nrpe1, and rdd, respectively) are slightly smaller than those listed in Additional file 2: Tables S1, S6, and S7 (1,399, 1,170, and 348), missing a few accessions representing variant gene models. This is because the VirtualPlant program  does not include all Arabidopsis gene models. (B) The Pol V mutant nrpe1 shows increased susceptibility to Fo infection whereas the Pol IV mutant nrpd1 is slightly more resistant to Fo than Col-0. The nrpd2a mutant, where both Pol IV and Pol V functions are disrupted, shows an intermediate disease response phenotype between nrpd1 and nrpe1. A total number of 84 to 174 plants were assayed for each line.