Comparative analysis of RNA interference and pattern-triggered immunity induced by dsRNA reveals different efficiencies in the antiviral response to Potato virus X

Plant antiviral responses induced by double-stranded RNA (dsRNA) include RNA interference (RNAi) and pattern-triggered immunity (PTI), but their relative contributions to antiviral defense are not well understood. We aimed at testing the impact of exogenous applied dsRNA on both layers of defense against Potato virus X expressing GFP (PVX-GFP) in Nicotiana benthamiana. Co-inoculation of PVX-GFP with either virus-specific (RNAi) or nonspecific dsRNA (PTI) showed that nonspecific dsRNA reduced virus accumulation in both inoculated and systemic leaves. However, nonspecific dsRNA was a poor inducer of antiviral immunity compared to a dsRNA capable to trigger the RNAi response, and plants became susceptible to systemic infection. Studies with a PVX mutant unable to move cell-to-cell indicated that the interference with PVX-GFP triggered by nonspecific dsRNA operated at the single-cell level. Next, we performed RNAseq analysis to examine similarities and differences in the transcriptome triggered by dsRNA alone or in combination with homologous and heterologous viruses. Enrichment analysis showed an over-representation of plant-pathogen signaling pathways, such as calcium, ethylene and MAPK signaling, which are typical of antimicrobial PTI. Moreover, the transcriptomic response to the homologous combination had a greater impact on defense than the heterologous combination, highlighting quantitative differences between RNAi and PTI immune responses. In addition, we provide genetic evidence that DICER-like2 and 4 as well as Argonaute2 were positively involved in PTI-based defense against PVX-GFP, and that dsRNA-induced PTI was enhanced by salicylic acid signaling. Together, these results further our understanding of plant antiviral defense, particularly the contribution of nonspecific dsRNA-mediated PTI.