DNA Methylation Analysis of the Response to Infection by Whole-Genome Bisulfite Sequencing.

DNA methylation is an important epigenetic mark associated with plant immunity, butlittle is known about its roles in viral infection of watermelon. We carried out whole-genomebisulfite sequencing of watermelon leaves at 0 h (ck), 48 h, and 25 days post-inoculation with (CGMMV). The number of differentially methylated regions(DMRs) increased during CGMMV infection and 2788 DMR-associated genes (DMGs) werescreened out among three libraries. Most DMRs and DMGs were obtained under the CHH context.These DMGs were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG)pathways of secondary biosynthesis and metabolism, plant-pathogen interactions, Toll-likereceptor signaling, and ABC transporters. Additionally, DMGs encoding PR1a, CaMs, calciumbindingprotein, RIN4, BAK1, WRKYs, RBOHs, STKs, and RLPs/RLKs were involved in thewatermelon-CGMMV interaction and signaling. The association between DNA methylation andgene expression was analyzed by RNA-seq and no clear relationship was detected. Moreover,downregulation of genes in the RdDM pathway suggested the reduced RdDM-directed CHHmethylation plays an important role in antiviral defense in watermelon. Our findings providegenome-wide DNA methylation profiles of watermelon and will aid in revealing the molecularmechanism in response to CGMMV infection at the methylation level.