Evolutionarily New Solanaceous DCL2 Family Members Acquire Functions in Tomato

RNA silencing is one of the major defence activities against viral pathogens in plants. Silencing signals are initiated by Dicer-like proteins (DCLs) to generate viral-derived small RNAs (sRNAs). Viral sRNAs are then loaded into Argonaute proteins to form an RNA-induced silencing complex to guide cleavage of target RNAs based on sequence homology. While the model regarding RNA silencing-mediated defence against viral pathogens is largely established based on extensive studies using the model plant Arabidopsis thaliana, there are diverse sets of silencing components in other plants, especially in domesticated crops. Here, we tracked the expansion of solanaceous-specific DCL2 genes during the course of evolution. We found that the DCL2a gene in tomato chromosome 6 is likely an evolutionarily new gene copy. We also found that DCL2b is more prone to be induced by viral pathogens in tomato plants, which is dependent on the combinations of cultivar and viral pathogen. Both DCL2a and DCL2b are critical to suppress the accumulation titre of a subviral agent, potato spindle tuber viroid (PSTVd). We noticed an unusually high accumulation of viral sRNAs shorter than 20 nt (16- to 19-nt in length) in viroid-infected tomato cv. Heinz 1706. Using synthetic small interfering RNAs, we demonstrated that shorter size sRNAs may also play a role in suppressing target RNAs, which can be interfered with by a viral suppressor of silencing, P19. Altogether, we provided further insights into the expansion of functional DCL2 family members in the Solanaceae family and their roles in combating viral and subviral agents.