WGBS and RNAseq from wild-type and slidm3-1 mutant tomato plants

DNA methylation and demethylation are crucial epigenetic regulatory mechanisms to control gene expression. DNA demethylases are enzymes that can actively and dynamically modify the methylation status of certain DNA regions, i.e. gene promoters. In plants, the IDM (Increased DNA Methylation) complex determines the sites where DNA should be demethylated. We created a null mutant of the IDM3 gene in tomato using the CRISPR/Cas9 genome editing system to reveal its function in plant development. The slidm3-1 mutant has a higher density of type I trichomes. We had the DNA methylome and the transcriptome sequenced from wild-type and slidm3 mutants. We identified the differentially methylated genomic regions and the differentially expressed genes in the mutant. We found that the tomato IDM3 was indeed a regulator of DNA methylation like its Arabidopsis homolog. We also identified some candidate genes the altered expression of which could explain the observed hairy phenotype.