Transcriptomic insights into fruiting body malformations in Lentinula edodes

Lentinula edodes (shiitake mushroom), the world's 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 performed 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. Our results revealed deformity-specific transcriptional signatures: the I vs. N4 and T vs. N3 phenotypes exhibited the most severe dysregulation (288 and 275 differentially expressed genes (DEGs), respectively), followed by P vs. N2 (185 DEGs), while H vs. N1 showed minimal changes (61 DEGs). Two DEGs (LENED_000547 and LENED_004546) were consistently identified across all four malformed types. They shared multiple conserved sequence motifs yet exhibited significant functional divergence, putatively acting as a nuclear-localized regulatory protein and a membrane-bound structural protein, respectively. Functional enrichment indicated 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. Kyoto Encyclopedia of Genes and Genomes analysis further highlighted disruptions in fructose/mannose metabolism, glutathione metabolism, and glycerolipid pathways. Weighted gene co-expression network analysis uncovered phenotype-correlated modules. Environmental stressors likely exacerbated these responses, as evidenced by the induced expression of several stress-responsive genes. This study suggests that intrinsic transcriptomic dysregulation drives L. edodes malformations, offering valuable targets for precision breeding and cultivation management. KEY POINTS: • Comparative transcriptomics provide preliminary molecular insights into four morphologically defined shiitake malformation phenotypes • Shared DEGs reveal conserved molecular drivers of abnormal development • Results guide breeding and cultivation strategies for improved shiitake yield.