Geminiviruses are plant ssDNA viruses that replicate through dsDNA intermediates and form
minichromosomes which carry the same epigenetic marks as the host chromatin. During the infection,
geminiviruses are targets of the post-transcriptional and transcriptional gene silencing machinery.
To obtain insights into the connection between virus-derived small RNAs (vsRNAs), viral genome
methylation and gene expression, we obtained the transcriptome, sRNAome and methylome from
the geminivirus Tomato yellow leaf curl virus-infected tomato plants. The results showed accumulation
of transcripts just at the viral ORFs, while vsRNAs spanned the entire genome, showing a prevalent
accumulation at regions where the viral ORFs overlapped. The viral genome was not homogenously
methylated showing two highly methylated regions located in the C1 ORF and around the intergenic
region (IR). The compilation of those results showed a partial correlation between vsRNA accumulation,
gene expression and DNA methylation. We could distinguish different epigenetic scenarios along
the viral genome, suggesting that in addition to its function as a plant defence mechanism, DNA
methylation could have a role in viral gene regulation. To our knowledge, this is the first report that
shows integrative single-nucleotide maps of DNA methylation, vsRNA accumulation and gene
expression from a plant virus.
