Systematic analysis of changes across different developmental stages of the mushroom Sarcomyxa edulis

Sarcomyxa edulis is a widely harvested mushroom of Northeastern Asia. Its development can be divided into six stages: growth of mycelium until occupying half the bag (B1), mycelium under low-temperature stimulation after occupying the entire bag (B2), appearance of mycelium in primordia (B3), primordia (B4), mycelium at the harvest stage (B5), and mature fruiting body (B6). Differentially expressed gene (DEG) analysis and weighted gene coexpression network analysis (WGCNA) are important bioinformatic methods for screening key genes. To explore the growth and development mechanisms of the mushroom S. edulis and clarify its genetic background, DEG and WGCNA analyses were combined to screen key genes at different developmental stages. From A1 to A6, respectively, 459, 97, 885, 169, 277, and 712 key genes were identified. Then the Gene Ontology (GO) terms and KEGG pathways of key genes were analyzed, and GO and KEGG analyses were performed on all genes across different periods using GSEA. In summary, the genes in A1 were mainly involved in amino sugar and nucleotide sugar metabolism, structural molecule activity, and oxidative phosphorylation. At the A2 stage, genes were mainly involved in peptidase activity, peroxidase activity, oxidoreductase activity, antioxidant activity, biosynthesis of secondary metabolites, and glycolysis and gluconeogenesis. A3 genes were involved in gene expression, RNA metabolism, spliceosome, RNA transport, and ribosome biogenesis. A4 genes were mainly involved in the biosynthesis of secondary metabolites, proteasome complex, cellular protein complex assembly, actin filament-based processes, oxidative phosphorylation, and carbon metabolism. The A5 stage genes were involved in the carbohydrate metabolic process, polysaccharide metabolic process, and the biosynthesis of secondary metabolites, leucine, isoleucine, and ABC transporters. Finally, A6 genes were mainly involved in the cell cycle, meiosis of yeast, MAPK signaling pathway, cellular response to DNA damage stimulus, DNA metabolic process, DNA replication, and DNA repair. The combination of multiple analyses provides us with an in-depth understanding of the network that regulates mushroom development.