Optimization of Juncao Substrate Formulation for Flammulina filiformis Cultivation: An Enzymatic and Transcriptomic Study

This study presents the transcriptomic analysis of Flammulina filiformis cultivated on an optimized substrate formulation incorporating Cenchrus fungigraminus as a partial replacement for traditional materials. Using the simplex-lattice method, the optimal substrate composition (20% C. fungigraminus and 28% corncobs) achieved a biological efficiency of 131.92% and improved fruiting body nutritional content. RNA-seq was performed to investigate the molecular mechanisms underlying enhanced yield and nutrient conversion efficiency. Transcriptomic profiling identified significant upregulation of genes involved in carbohydrate metabolism and cellular processes under the optimized formulation. These findings provide insights into how alternative substrates regulate carbon and nitrogen metabolism at the transcriptional level, contributing to resource-efficient cultivation strategies.