Transcriptomic Dissection of Fruiting Body Malformations in Lentinula edodes Reveals Intrinsic Dysregulation of Gene Expression

Lentinula edodes, the world's second most cultivated edible fungus, frequently develops malformed fruiting bodies during commercial cultivation, leading to significant economic losses. To elucidate the molecular basis of these deformities, we conducted a comparative transcriptome analysis of four distinct malformation types--marginal depression (H), central protrusion (P), twinning (T), and irregularity (I)--versus normal controls (N1-N4) under identical cultivation conditions. Furthermore, two DEGs (LENED_000547 and LENED_004546) were consistently identified across all four malformed types compared to their respective controls, underscoring their potential critical role in malformation development. We observed that all malformed types consistently exhibited downregulation of genes associated with structural molecule activity, nucleotide binding, and transferase activity, suggesting a fundamental compromise in cellular integrity and metabolism. Conversely, genes involved in carbohydrate metabolism, transmembrane transport, and hydrolase activity were upregulated, suggesting altered nutrient allocation and cell wall dynamics. KEGG analysis further highlighted disruptions in fructose/mannose metabolism, glutathione metabolism, and glycerolipid pathways. Weighted gene co-expression network analysis (WGCNA) uncovered phenotype-correlated modules. Environmental stressors likely exacerbated these responses, as evidenced by the induced expression of several stress-responsive genes.