DNA Methylation Analysis of the Citrullus lanatus Response to Cucumber Green Mottle Mosaic Virus Infection by Whole-Genome Bisulfite Sequencing

Abstract

DNA methylation is an important epigenetic mark associated with plant immunity, but little is known about its roles in viral infection of watermelon. We carried out whole-genome bisulfite sequencing of watermelon leaves at 0 h (ck), 48 h, and 25 days post-inoculation with Cucumber green mottle mosaic virus (CGMMV). The number of differentially methylated regions (DMRs) increased during CGMMV infection and 2788 DMR-associated genes (DMGs) were screened 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-like receptor signaling, and ABC transporters. Additionally, DMGs encoding PR1a, CaMs, calcium-binding protein, RIN4, BAK1, WRKYs, RBOHs, STKs, and RLPs/RLKs were involved in the watermelon–CGMMV interaction and signaling. The association between DNA methylation and gene 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 CHH methylation plays an important role in antiviral defense in watermelon. Our findings provide genome-wide DNA methylation profiles of watermelon and will aid in revealing the molecular mechanism in response to CGMMV infection at the methylation level.

Alterations of Rice (Oryza sativa L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus

“…We observed a total of 408,352 CGIs (317 053 hypermethylated and 91,299 hypomethylated, respectively) ( Figure 2 B). There were more hypermethylated genes than hypomethylated genes which was consistent with the previous studies [ 15 ]. The DMR-associated genes obtained according to differential methylation statistics in 2000 regions upstream of the transcription start site of the gene were classified into three groups according to biological process, cellular component and molecular function based on rice GO annotation information.…”

“…DEGs in three biological replicates were similar, confirming the reliability of the data ( Figure 3 C,D). 181 DEGs were assigned to the 20 canonical reference pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) that may play important roles in plants responses to various viruses [ 15 ]. 38 DEGs participated in plant-pathogen interactions and 33 DEGs were involved in plant hormone signal transduction ( Figure 3 E).…”

“…Unlike DNA viruses, RNA viruses possess scarcely methylated RNA genomes for replication [ 10 ]. DNA methylation regulates the expression of plant disease resistance genes to respond to the infection of RNA viruses [ 13 , 14 , 15 ]. For example, DNA (de)methylation altered the susceptibility/resistance of Arabidopsis plants to tobacco rattle virus (TRV) infection by regulating the expression of disease resistance genes [ 16 ].…”

Cytosine methylation in the promoter region of genes involved in cellular oxidation equilibrium pathways affects rice heat tolerance

“…The consistent demethylation of the cytosines in the promoter region of PPR, the consistent methylation of the cytosines in the downstream region of bZIP, as well as the stable methylation state in the downstream regions of MYB and C2H2 contribute to rice heat tolerance [46]. Several additional TFs, including flowering control locus A (FCA), bZIP, tryptophan-arginine-lysinetyrosine (WRKY), APETALA2 (AP2), cysteine 8-cysteine 5 or cysteine 3-histidine-type zinc finger protein (C8C5C3H), and DNA binding with one finger protein (Dof), were also reported to be regulated by DNA methylation in plants [49][50][51]. The post-transcriptional regulator FCA, which has two RNAbinding motifs (RRMs), upregulates the gene mitogen-activated protein kinase 5 lacking an intact kinase domain (OstMAPKKK5).…”

RdDM pathway is required forTobamovirus-induced symptomatology production

“…In recent years, researchers have published several studies about the effects of DNA methylation on antiviral defense. The infection by TRV and Cucumber Mottled Green Mosaic Virus (CGMMV) in Arabidopsis and watermelon, respectively, produces a deregulation of key components of the RdDM machinery, thus evidencing an important role of methylation in antiviral defense (Diezma-Navas et al ., 2019; Sun et al ., 2019). Another study revealed a novel regulatory mechanism, whereby Cotton Leaf Curl Multan virus (CLCuMuV) C4 protein suppresses TGS and PTGS mediated by SAMS (a central enzyme in the methyl cycle), which leads to an improved viral infection in the plant (Ismayil et al ., 2018).…”