Combined Transcriptomic and Metabolomic Analyses of the Response of Ganoderma lucidum to Elevated CO₂

Carbon dioxide (CO₂) is a key environmental factor that regulates the morphology of fruiting bodies in edible fungi. High CO₂ concentrations often lead to the formation of antler-shaped abnormal fruiting bodies in Ganoderma lucidum. Yet, the molecular response mechanisms underlying this process remain unclear. To address this gap, this study integrated transcriptomics and untargeted metabolomics to compare the transcriptional and metabolic profiles of G. lucidum fruiting bodies at three growth stages, cultivated under both normal (0.04%) and high CO₂ concentrations (0.3%). Metabolomic analysis revealed that, compared to the control groups, 387, 337, and 445 differentially accumulated metabolites were identified in the elevated-CO₂ groups, respectively. Moreover, high CO₂ concentrations led to a widespread down-regulation of various amino acids biosynthesis, accompanied by a marked accumulation of specific triterpenoids and steroids. This indicates distinct metabolite accumulation patterns in the fruiting bodies of G. lucidum cultivated under elevated CO₂. Furthermore, transcriptomic analysis showed that, at a key stage of fruiting body development, high CO₂ concentrations adversely affected gene expression of cell cycle-yeast, proteasome, DNA replication, mismatch repair, and meiosis-yeast pathways, which may decrease the cell division ability and prevent normal pileus development. Meanwhile, the differential expression of genes related to CO₂ signal perception and transduction and cell wall remodeling provided a molecular basis for the morphogenesis of the antler-type fruiting bodies. Overall, this study delineates a multi-layered, multi-pathway regulatory network through which high CO₂ concentrations affect the development and metabolism of G. lucidum, encompassing energy metabolism reprogramming, inhibition of cell division, and cell wall remodeling. This provides new insights into CO₂ as an environmental signal in fungal development and a theoretical basis for optimizing G. lucidum cultivation practices.