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 <i>Ganoderma lucidum</i>. 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 <i>G. lucidum</i> 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 <i>G. lucidum</i> 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 <i>G. lucidum</i>, 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 <i>G. lucidum</i> cultivation practices.