Transcriptomic and metabolomic analyses reveal the role of flavonoids in ectomycorrhizal symbiosis.

Flavonoids are major plant secondary metabolites that mediate diverse plant–microbe interactions, including ectomycorrhizal (ECM) symbioses. However, their regulatory roles during ECM development remain poorly understood. Here, we investigated whether inoculation with Suillus bovinus alters flavonoid biosynthesis in Pinus yunnanensis roots and assessed how these flavonoids on fungal growth and gene expression. We applied exogenous flavonoids to S. bovinus mycelia to investigate fungal transcriptional and metabolic responses. Following inoculation, differentially expressed genes in P. yunnanensis roots were significantly enriched in the flavonoid biosynthesis pathway. Key enzyme-coding genes, including PAL, CHS, CHI, F3H, and FLS, were upregulated, and this was associated with increased flavonoid accumulation and enhanced antioxidant capacity. In S. bovinus, exogenous flavonoids promoted mycelial growth and induced metabolic adjustments related to carbohydrate and amino acid utilization. Several small secreted protein-related genes showed transcriptional responses to flavonoid exposure, indicating potential transcriptional modulation, although their specific roles in symbiosis remain unclear. These findings indicate that flavonoids may contribute to reciprocal interactions between host roots and ECM fungi and provide a molecular basis for further investigation.