Multi‑omics analysis of fire blight infection in Pyrus betulifolia provides insights into genes, proteins and metabolites involved in pathogenesis

Background Fire blight caused by Erwinia amylovora severely impairs pear cultivation globally. To uncover the molecular defense mechanisms of P. betulifolia against fire blight, this study conducted integrated transcriptomic, proteomic and metabolomic analyses on healthy and infected leaf and branch tissues. Results A large number of differentially expressed genes, proteins and metabolites were identified in infected leaves and branches, respectively. The 36 common differently expressed gene/protein pairs and 89 differently expressed metabolites were isolated in both of leaves and branches. KEGG enrichment demonstrated that infected leaves mainly activated plant-pathogen interaction pathway, while branches relied on terpenoid, amino acid and lipid metabolism reprogramming. Transcription factor WRKY25 , pathogenesis-related ( PR ) genes and mitogen-activated protein kinase MPK3 , and their corresponding proteins might play critical regulatory functions in plant-pathogen interaction pathway. Multi-omics analysis revealed that flavonoid biosynthesis pathways were strongly induced, leading to massive accumulation of antibacterial flavonoids following pathogen infection. Key structural genes, including PAL , 4CL , CHS and CHI , were substantially upregulated. Consistently, flavones such as chrysin and galangin exhibited uniform and robust induction in both leaves and branches, with markedly higher induction levels in branches. Conclusions This study systematically elucidates the conserved and tissue-specific molecular mechanisms of P. betulifolia defending against fire blight, providing vital multi-omics insights and a theoretical basis for breeding fire blight-resistant pear varieties.