Comparative Transcriptomics of Flammulina filiformis Suggests a High CO2 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 CO₂ is still unknown. In this study, the young fruiting bodies of a popular commercial mushroom Flammulina filiformis were cultivated under different CO₂ concentrations. In comparison to the low CO₂ concentration (0.05%), the pileus expansion rates were significantly lower under a high CO₂ concentration (5%). Transcriptome data showed that the up-regulated genes enriched in high CO₂ concentration treatments mainly associated with metabolism processes indicated that the cell metabolism processes were active under high CO₂ 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 CO₂. Transcriptome and qRT-PCR analyses demonstrated that a high CO₂ 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 CO₂, which could provide a theoretical basis for a CO₂ management strategy in mushroom cultivation.

DcC4H and DcPER Are Important in Dynamic Changes of Lignin Content in Carrot Roots under Elevated Carbon Dioxide Stress

In our study, isobaric tags for relative and absolute quantification (iTRAQ) was conducted to determine the significantly changed proteins in the fleshy roots of carrots under different carbon dioxide (CO₂) treatments. A total of 1523 proteins were identified, of which 257 were differentially expressed proteins (DEPs). On the basis of annotation analysis, the DEPs were identified to be involved in energy metabolism, carbohydrate metabolism, and some other metabolic processes. DcC4H and DcPER, two lignin-related proteins, were identified from the DEPs. Under elevated CO₂ stress, both carrot lignin content and the expression profiles of lignin biosynthesis genes changed significantly. The protein-protein interactions among lignin-related enzymes proved the importance of DcC4H and DcPER. The results of our study provided potential new insights into the molecular mechanism of lignin content changes in carrot roots under elevated CO₂ stress.