Hypsizygus marmoreus is a representative edible mushroom with low-temperature fruiting after a long postripening (LFLP). Clarifying the mechanism of LFLP and applying a rigorous low-temperature-limited process will optimize the mushroom cultivation process. This study performed an integrative multi-omics analysis of the molecular mechanism of LFLP in combination with genetic, physiological, and cultivation confirmation. The results showed that the amino acid content was increased during LFLP, mainly arginine. pH analysis showed acidification in the postripening stage and alkalization in the substrates of the reproductive growth stage. An enzyme activity test confirmed the increased enzyme activity of arginase and citrate synthase in the postripening stage. Weighted gene coexpression network analysis of the transcriptome and metabolomics indicated that pH variation is correlated mainly with changes in citrate and arginine. Multi-omics reveals a straightforward way of providing enriched materials for amino acid biosynthesis, namely, synergistically elevating citric acid and arginine through enhanced activity of the arginine synthesis branch pathway in the citrate cycle. Our study confirmed that GCN2 mediated metabolic adaptation by enhancing protein translation, highlighting its regulatory role during LFLP. Exogenously added citric acid and arginine shortened the postripening period by 10 days and increased the fruiting body yield by 10.2~15.5%. This research sheds light on the molecular mechanism of LFLP in H. marmoreus and highlights the promising application of nutrient accumulation in high-efficiency cultivation.

In Volvariella volvacea, an important species of edible mushroom, cryogenic autolysis is a typical phenomenon that occurs during abnormal metabolism. Analysis of gene expression profiling and qPCR showed that chilling stress (CS) significantly and continuously upregulated only one type of Argonaute in V. volvacea, i.e., VvAgo1. Structural and evolutionary analysis revealed that VvAgo1 belongs to the Ago-like family, and its evolution has involved gene duplication, subsequent gene loss, and purifying selection. Analysis of its interaction network and expression suggested that CS triggers VvAgo1-mediated miRNA-like RNA (milRNA) biogenesis in V. volvacea V23 but not in VH3 (a composite mutant strain from V23 with improved CS resistance). Small RNA sequencing and qPCR analysis confirmed that CS triggered the increased milRNA expression in V23 and not in VH3. The predicted target genes of the increased milRNAs were enriched in several pathways, such as signal transduction and ubiquitination. Heatmap analysis showed that CS altered the expression profile of milRNAs with their target genes related to signal transduction and ubiquitination in V23. Combined analysis of transcriptome and proteome data confirmed that most of the target genes of the increased milRNAs were not translated into proteins. Our observations indicate that CS might trigger VvAgo1-mediated RNAi to facilitate the cryogenic autolysis of V. volvacea.

DNA methylation, a cornerstone of epigenetic regulation, governs critical biological processes including transcriptional modulation, genomic imprinting, and transposon suppression through chromatin architecture remodeling. Recent advances have revealed that aberrant methylation patterns—characterized by spatial-temporal dysregulation and stochastic molecular noise—serve as key drivers of diverse pathological conditions, from oncogenesis to neurodegenerative disorders. However, the field faces dual challenges: (1) current understanding remains fragmented due to the inherent spatiotemporal heterogeneity of methylation landscapes across tissues and developmental stages, and (2) mechanistic insights into non-canonical methylation pathways (particularly 6mA) in non-mammalian systems are conspicuously underdeveloped. This review systematically synthesizes the evolutionary-conserved versus species-specific features of 5-methylcytosine (5mC) and N6-methyladenine (6mA) regulatory networks across three biological kingdoms. Through comparative analysis of methylation/demethylation enzymatic cascades (DNMTs/TETs in mammals, CMTs/ROS1 in plants, and DIM-2/DNMTA in fungi), we propose a unified framework for targeting methylation-associated diseases through precision epigenome editing, while identifying critical knowledge gaps in fungal methylome engineering that demand urgent investigation.

Postharvest Flammulina filiformis is prone to quality degradation, adversely impacting its commercial value. Cordyceps militaris, rich in antioxidant and antibacterial components, shows promise as a natural biological preservative. This study aimed to explore the potential of C. militaris extract (CME) as a preservative for F. filiformis. Through analyzing indicators such as browning, stipe elongation, and cap diameter, this study confirmed the effectiveness of CME in delaying oxidation and inhibiting microbial growth during storage. Additionally, transcriptome analysis revealed that CME modulated gene expression in F. filiformis, enhancing its antioxidant defense mechanisms. The results demonstrated that CME could effectively extend the shelf life of F. filiformis, providing valuable insights into preservation strategies for this and other edible fungi.

This study investigated the preservative effect and molecular mechanism of cold-air pre-cooling (CAP) combined with storage at 15 °C/85% relative humidity on Volvariella volvacea. CAP significantly reduced weight loss and browning, maintained moderate respiratory intensity, minimised malondialdehyde accumulation and polyphenol oxidase activity, and preserved higher firmness and soluble-protein content, extending the shelf life by 4 d. An analysis of energy metabolism indices revealed that CAP increased mitochondrial quantity, membrane potential, and ATP content. Specifically, CAP restricted the tricarboxylic acid (TCA) cycle rate by downregulating the activities of succinate dehydrogenase, isocitrate dehydrogenase, and citrate synthase. Additionally, CAP prevented the peak activation of respiratory complex I, while sustaining optimal activity of complexes III and IV, thereby stabilising intracellular ATP levels. Transcriptomic analysis further indicated that CAP suppressed the activity of the TCA cycle and oxidative phosphorylation pathways during postharvest storage. Quantitative real-time PCR (qPCR) validated the downregulation of genes associated with respiratory complexes after CAP treatment. In conclusion, CAP maintained the postharvest quality of V. volvacea by preserving energy metabolism homeostasis, providing a theoretical basis for its application in edible mushroom preservation.