Integrated Transcriptome and Metabolome Analysis Dissecting the Interaction between Cultivated Solanum lycopersicum and Tomato Brown Rugose Fruit Virus

To elucidate its interaction with tomato (Solanum lycopersicum), we performed an integrated transcriptomic and metabolomic analysis. Compared to mock-inoculated plants, we identified 4,477 differentially expressed genes and 91 differentially accumulated metabolites.

Notably, L‑Histidine was significantly upregulated while the flavonol quercetin was downregulated in response to infection. Functional validation via exogenous application revealed that L‑Histidine enhanced the expression of defense-related genes and activated the ethylene signaling pathway, whereas quercetin treatment upregulated genes involved in the MAPK signaling cascade. Collectively, our integrated multi-omics analysis and functional validation reveal that L‑Histidine acts as a positive immune inducer while quercetin contributes to antiviral defense through distinct signaling pathways.