Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

Background Cucumber green mottle mosaic virus (CGMMV) causes substantial global losses in cucurbit crops, especially watermelon. N6-methyladenosine (m(6)A) methylation in RNA is one of the most important post-transcriptional modification mechanisms in eukaryotes. It has been shown to have important regulatory functions in some model plants, but there has been no research regarding m(6)A modifications in watermelon. Results We measured the global m(6)A level in resistant watermelon after CGMMV infection using a colorimetric method. And the results found that the global m(6)A level significantly decreased in resistant watermelon after CGMMV infection. Specifically, m(6)A libraries were constructed for the resistant watermelon leaves collected 48 h after CGMMV infection and the whole-genome m(6)A-seq were carried out. Numerous m(6)A modified peaks were identified from CGMMV-infected and control (uninfected) samples. The modification distributions and motifs of these m(6)A peaks were highly conserved in watermelon transcripts but the modification was more abundant than in other reported crop plants. In early response to CGMMV infection, 422 differentially methylated genes (DMGs) were identified, most of which were hypomethylated, and probably associated with the increased expression of watermelon m(6)A demethylase gene ClALKBH4B. Gene Ontology (GO) analysis indicated quite a few DMGs were involved in RNA biology and stress responsive pathways. Combined with RNA-seq analysis, there was generally a negative correlation between m(6)A RNA methylation and transcript level in the watermelon transcriptome. Both the m(6)A methylation and transcript levels of 59 modified genes significantly changed in response to CGMMV infection and some were involved in plant immunity. Conclusions Our study represents the first comprehensive characterization of m(6)A patterns in the watermelon transcriptome and helps to clarify the roles and regulatory mechanisms of m(6)A modification in watermelon in early responses to CGMMV.