Epigenetic changes of Nicotiana tabacum in response to viral infection through single-base resolution methylomes

Plants have evolved into multiple mechanisms to respond to viral infection. These responses have been studied in detail at the level of host immune response and antiviral RNA silencing (RNAi). However, the possible epigenetic reprogramming has not been thoroughly investigated. Cytosine DNA methylation is one form of epigenetic modification that regulates gene expression and maintains genome integrity. Here we performed reduced representation bisulfite sequencing (RRBS) on tissues of cucumber mosaic virus (CMV) infected Nicotiana tabacum at various stages (symptom development and clearance). Differential methylated regions are enriched with CHH hypomethylated sequence contexts, most of which are located on the gene body to regulate expression. Methylation change in the argonaute and defense protein revealed the important role of dynamic methylation changes for viral clearance. Methylation-expression relationships are identified to be required for immune response and cellular components, which is necessary to establish the proper defense response for infection and symptom recovery.