Relative abundance of host siRNAs, and their distribution in different size classes, was severely altered at 21 dpi and, at a lesser extent, at 30 dpi, as compared to healthy plants. MicroRNAs (miRNAs) accounted for a 2.8% of total reads mapping to the tomato genome in mock-inoculated plants, and this figure raised up to 8.5% in infected plants at 21 dpi. Fifty-seven miRNA species showed at least a two-fold increase and 56 at least a two-fold decrease in infected vs. healthy plants at 21 dpi, and most of them were similarly altered at both timepoints. MiRNA target genes, whose expression regulation was shown or predicted to be differentially modulated in infected plants, belong to specific functional categories involving transcription factors, kinases and genes with oxidoreductase activity, which may partially explain the disease symptoms induced by the virus. Abundant secondary siRNAs (e.g. phasiRNAs), depending on an upstream small RNA trigger and subsequent RDR and DCL activities, were induced by virus infection and shown to be biologically active by driving cleavage of pathogen-responsive genes, such as receptor-like kinases (RLKs).
