Dual RNA-Seq Reveals Molecular Interactions Between Alternaria alternata and Cucumis melo During Postharvest Infection.

Alternaria alternata causes major postharvest losses in melons. This dual RNA-seq study analyzed transcriptomic dynamics in both A. alternata strain A2022 and melon during infection. Genomic analysis revealed two conditionally dispensable chromosomes (CDCs) containing host-specific toxin genes, including a T1PKS cluster for βenone biosynthesis. Fungal transcriptomics identified upregulated virulence pathways: MAPK signaling (18 genes), autophagy (17 genes), and lipid metabolism. Melon mounted a biphasic defense: early lignin deposition via phenylpropanoid biosynthesis (15 genes) and late jasmonic acid/MAPK-mediated responses. Competitive nutrient acquisition emerged, with fungal amino acid transporters opposing host nitrogen metabolism. These findings reveal A. alternata's genomic plasticity and melon's layered resistance, suggesting RNAi-based silencing of CDC virulence genes or breeding for enhanced lignin/jasmonate pathways as sustainable control strategies.