Comparative Transcriptomics of Flammulina filiformis Suggests a High CO(2) Concentration Inhibits Early Pileus Expansion by Decreasing Cell Division Control Pathways

Carbon dioxide is commonly used as one of the significant environmental factors to control pileus expansion during mushroom cultivation. However, the pileus expansion mechanism related to CO(2) is still unknown. In this study, the young fruiting bodies of a popular commercial mushroom Flammulina filiformis were cultivated under different CO(2) concentrations. In comparison to the low CO(2) concentration (0.05%), the pileus expansion rates were significantly lower under a high CO(2) concentration (5%). Transcriptome data showed that the up-regulated genes enriched in high CO(2) concentration treatments mainly associated with metabolism processes indicated that the cell metabolism processes were active under high CO(2) conditions. However, the gene ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with cell division processes contained down-regulated genes at both 12 h and 36 h under a high concentration of CO(2). Transcriptome and qRT-PCR analyses demonstrated that a high CO(2) concentration had an adverse effect on gene expression of the ubiquitin–proteasome system and cell cycle–yeast pathway, which may decrease the cell division ability and exhibit an inhibitory effect on early pileus expansion. Our research reveals the molecular mechanism of inhibition effects on early pileus expansion by elevated CO(2), which could provide a theoretical basis for a CO(2) management strategy in mushroom cultivation.