Integrated transcriptomic and metabolomic analyses reveal hormone-mediated crosstalk during potato virus Y and potato spindle tuber viroid co-infection

Plants often face multiple pathogen attacks at once, but how they handle these complex infections at the molecular level is not well understood. This study uses transcriptomic and metabolomic analyses to explore the interaction between potato virus Y (PVY), a protein-coding RNA virus, and potato spindle tuber viroid (PSTVd), a non-coding RNA pathogen, which could infect potato plants together. Samples from different potato fields showed a strong prevalence of PVY, whereas PSTVd exhibited low occurrence compared to PVY but frequently co-occurred with it, indicating potential interactions between these pathogens. Observations of plant symptoms confirmed a PVY dominant role, causing severe stunting and yellowing, while PSTVd milder effects were hidden in co-infected plants. Transcriptomic data revealed PVY broadly alters plant processes like photosynthesis, carbon use, and immune responses, while PSTVd targets specific pathways, such as protein modification and plant-pathogen interactions. Co-infection boosted these effects, triggering strong increases in defense-related TF, e.g., WRKYs, NACs, MYCs, and hormone signalling. Metabolite analysis showed major changes in hormones, especially cytokinins and jasmonates, with zeatin production as a key shared pathway. Weighted Gene Co-expression Network Analysis (WGCNA) identified unique gene groups for each infection, with co-infection showing enhanced immune and metabolic activity. Integrated gene-metabolite networks confirmed PVY leading role, linking key genes, e.g., AHP1/4, PYL1/8, COI1, to hormones like cytokinin, jasmonoyl-isoleucine and abscisic acid. These findings suggest PVY drives strong immune responses, while PSTVd may rely on PVY suppression of plant defenses to survive, offering new insights into managing complex plant diseases. • PVY dominates disease outcomes and enables PSTVd persistence during co-infection. • PVY drives global transcriptional reprogramming, whereas PSTVd induces targeted host responses. • Co-infection synergistically enhances immune transcription factors and hormone signaling. • Integrated multi-omics identifies PVY-centered cytokinin and jasmonate networks underlying pathogen crosstalk.