Integrative analysis of metabolome and transcriptome reveals new insights into the formation and regulation of major components of G. leucocontextum and G. lucidum

Ganoderma is a class of medicinal fungi with diverse medicinal effects, of which triterpenoids are one of the main pharmacologically active substances. In this study, sporocarps of two Ganoderma species ( Ganoderma leucocontextum , a newly discovered species, and Ganoderma lucidum , a traditional medicinal species) at five different developmental stages were used as test materials for joint transcriptomic and metabolomic analyses. Metabolomic analysis via ultra-high performance liquid chromatography tandem mass spectrometry identified a total of 514 differential metabolites (screened by VIP ≥ 1 and P < 0.05). Among these, triterpenoids were the primary class of differentially abundant metabolites between the two species: G. leucocontextum consistently contained higher levels of ganoleucoin during development, while G. lucidum maintained higher levels of ganoderic acid. Transcriptomic analysis yielded 227.61 Gb of clean data ( Q 30 base percentage > 93%), with 228,593 significantly differentially expressed genes identified across the five developmental stages. Most genes in the triterpenoid synthesis pathway (including several Ganoderma -specific CYP450 family genes) were more highly expressed in G. lucidum . RT-qPCR validation of six key DEGs confirmed that their expression trends were consistent with transcriptomic data. Additionally, six putative transcription factors (belonging to HSF and GNAT families) potentially involved in Ganoderma triterpene metabolism were identified. Our findings provide data sets on dynamic gene expression and differential metabolites during the development of the two Ganoderma species, laying a foundation for subsequent in-depth research. IMPORTANCE Since forward genetic dissection of favorable traits is a time-consuming and arduous task in basidiomycete mushrooms, comprehensive analysis using omics technologies has become a feasible option. In this study, five different sporocarp developmental stages (S1–S5) of Ganoderma leucocontextum and Ganoderma lucidum were selected, and through combined transcriptome and metabolome analysis, we aimed to preliminarily clarify the differences in active ingredients and key genes related to active substances in G. leucocontextum compared with traditional Ganoderma ( G. lucidum ; Chizhi).