Minglei Li

Buchwaldoboletus xylophilus is a rare saprotrophic edible mushroom in the Boletaceae and is the second bolete species to have been successfully cultivated artificially, yet its developmental molecular regulation remains unexplored. We integrated RNA-seq transcriptomics and untargeted LC-MS/MS metabolomics across five developmental stages (A–E), applying differential expression, alternative splicing, ceRNA network construction, WGCNA, machine learning, consensus clustering, and O2PLS joint modelling. Transcriptomic analysis revealed that the mycelium-to-primordium transition (stage A to C) showed the most drastic reprogramming, with 2233 differentially expressed genes, while metabolomic comparison between stage A and E revealed overwhelmingly upregulated metabolites (184 up vs. 10 down), indicating asymmetric regulation between the two omics layers. Notably, mutually exclusive exon splicing events exhibited high functional significance, and all top ceRNA hubs were lncRNAs. Unsupervised consensus clustering validated the molecular distinctness of the sampled stages. Metabolite enrichment highlighted antioxidant functions and ABC transporter pathways, and O2PLS integrative modelling confirmed a strong shared developmental signal between transcriptome and metabolome. This study provides the first multidimensional molecular atlas for B. xylophilus, revealing a non-linear developmental programme, transcriptome–metabolome decoupling, and a central role of antioxidant defence throughout development. Our findings offer mechanistic clues regarding the evolutionary transition from ectomycorrhizal to saprotrophic lifestyles in the Boletaceae and establish a multi-omics foundation for the molecular breeding of this emerging edible and medicinal mushroom.

Plant pathogens pose a severe threat to global agricultural production, and their pathogenicity is closely linked to the biosynthesis of secondary metabolites. Basidiomycete within the family Ustilaginaceae represent significant plant pathogens, among which Ustilago maydis, as a model species, has been extensively studied for its secondary metabolites. However, the biosynthetic potential of other species within this family remains poorly understood. In this study, we conducted whole-genome bioinformatic analyses of 16 Ustilaginaceae species, including U. maydis, to systematically identify the distribution of biosynthetic gene clusters (BGCs), core gene domain compositions, and interspecies similarities. A total of 181 predicted BGCs were identified, averaging approximately 11 per species. BGCs for mannosylerythritol lipids (MELs), siderophores, and itaconic acid, as well as the melanin-associated genes pks1 and pks2, were widely distributed across most species. Conversely, an additional melanin biosynthetic gene cluster was found exclusively in U. maydis strain 521, indicating species-specific occurrence. Furthermore, this study identified a novel class of polyketide synthase (PKS) gene clusters with uncharacterized functions across 15 species, exhibiting high sequence and structural conservation between species. These findings reveal the rich metabolic diversity and species-specific biosynthetic potential of Ustilaginaceae, and by using U. maydis as a reference model, we highlight several BGCs (e.g., for MELs, siderophores, itaconic acid, and melanin) that are known to contribute to virulence or pathogenicity in plant hosts. This provides new insights into their pathogenic mechanisms.

The severe continuous cropping obstacles in Morchella cultivation, driven primarily by soil microecological imbalance, critically constrain the sustainable development of the industry. To address this challenge, this study evaluated the efficacy of rotary tillage, calcium cyanamide (CaCN₂), and organic fertilizer, applied individually and in combination, in mitigating these obstacles and explored the underlying microbial mechanisms. The soil was treated on 5 August 2024, and soil samples were collected on 5 October 2024. Four treatments were established: continuous cropping control (CK), rotary tillage (XGX), rotary tillage combined with calcium cyanamide (MPD), and rotary tillage combined with calcium cyanamide and organic fertilizer (MPX). Soil chemical properties were analyzed in conjunction with metagenomic sequencing to characterize the responses of soil properties and microbial communities, including both eukaryotic and bacterial taxa. The results indicated that the MPD treatment showed a relatively pronounced effect in enhancing key soil fertility indicators, including soil organic matter (OM), total nitrogen (TN), available nitrogen (AN), available potassium (AK), and total phosphorus (TP). All amendments significantly altered microbial community structures. Specifically, the integrated MPX treatment effectively reduced the relative abundance of the pathogenic fungus Olpidium while maintaining higher overall microbial diversity. It also significantly promoted the abundance of Morchella itself and beneficial bacterial phyla such as Actinomycetota and Pseudomonadota. Redundancy analysis identified AN and AK as the primary drivers of eukaryotic community variation, whereas Availa-ble phosphorus (AP) and potential of hydrogen (pH) were the key factors shaping the bacterial community. The results indicated that MPD was the showed relatively pronounced effectiveness in rapidly improving soil fertility and suppressing pathogenic fungi. In contrast, MPX showed relatively better performance in optimizing microbial community structure, enhancing microbial diversity, and strengthening overall ecological stability. These two treatments exhibited distinct advantages in soil chemical improvement and microbial community regulation, respectively, thereby providing alternative practical strategies and a theoretical basis for the ecological management of continuous-cropping obstacles in Morchella cultivation. It should be noted that this study did not include treatments with calcium cyanamide alone, organic fertilizer alone, or their combined application without rotary tillage. This is primarily because rotary tillage is a standard land preparation practice in Morchella cultivation, and the use of soil amendments without accompanying tillage is rarely adopted under practical production conditions.

With the continuous expansion of Pleurotus ostreatus cultivation, substantial quantities of post-harvest spent mushroom substrate (SMS) are generated. Improper disposal of this organic waste poses potential threats to soil health, including contamination and ecological imbalance. Consequently, a rigorous safety assessment is indispensable to support the sustainable and agronomically viable utilization of SMS as a soil amendment. In this study, P. ostreatus SMS was subjected to sterilized and non-sterilized treatments, and a controlled co-culture system integrating P. ostreatus mycelium with wheat was established. This system facilitated a comprehensive evaluation of residual mycelium impacts on wheat growth and development at phenotypic, cytological, and non-targeted metabolomics (LC-MS) levels. Results demonstrated that direct field application of non-sterilized SMS severely compromised wheat performance, inducing root necrosis and significantly reducing grain set. Comparative experiments confirmed that non-sterilized SMS—not its sterilized counterpart—exerted pronounced phytotoxic effects, markedly inhibiting seedling growth and triggering wilting symptoms. To elucidate the temporal dynamics of mycelial interaction, wheat seedlings were inoculated with viable P. ostreatus mycelium and co-cultured for seven days. Under these conditions, the mean root length of the control group (10.82 cm) was approximately threefold that of the treatment group. Histopathological analysis revealed a progressive infection pattern initiating at the root apex and extending basipetally; prolonged exposure ultimately caused complete root system collapse. Scanning electron microscopy further showed extensive mycelial colonization on infected root surfaces, accompanied by characteristic cellular damage—including severe cell wall wrinkling and widespread cell death. LC-MS profiling identified 1867 annotated compounds. Comparative analysis revealed significant dysregulation of secondary metabolism, with 495 metabolites upregulated and 419 metabolites downregulated in the treatment group. Collectively, these findings provide robust evidence that unprocessed P. ostreatus SMS poses tangible agronomic risks upon direct soil application. This study establishes a critical scientific foundation for developing safe, evidence-based protocols for the valorization and integrated management of SMS.

The genus Auricularia, and specifically the species A. auricula, is a globally significant edible fungus with a long history of cultivation and notable nutritional and medicinal properties. This review systematically examines the taxonomic classification, morphological and physiological characteristics, and bioactive components (such as polysaccharides, melanin, proteins and polyphenols) of A. auricula, as well as their pharmacological effects and industrial applications. Recent molecular biological advances have clarified taxonomic uncertainties, including the reclassification of ‘heimuer’ as A. cornea, and emphasized the species’ genetic diversity. A. auricula thrives in temperate and subtropical regions, with cultivation techniques evolving from traditional wood log inoculation to modern substrate-based methods. However, sustainability challenges persist, including reliance on virgin wood substrates and the need for improved spent substrate management. The fungus exhibits remarkable nutritional properties, with polysaccharides (up to 66.1% of dry weight) demonstrating hypoglycemic, antitumor, immunomodulatory, and antioxidant activities. Melanin and proteins further contribute to hepatoprotection, antimicrobial effects, and metabolic regulation. Industrial applications of Auricularia species extend beyond food into pharmaceuticals and functional materials. Polysaccharides are explored as drug carriers, while melanin shows promise in antioxidant and antibacterial formulations. Despite these advances, gaps remain in understanding the mechanistic basis of bioactive compound functions and optimizing cultivation for sustainable production. Future research should integrate multi-omics approaches to elucidate genetic regulation, enhance substrate formulations, and develop value-added products. This review underscores the potential of Auricularia species as a functional food and biotechnological resource, advocating for interdisciplinary efforts to address current challenges and unlock its full industrial potential.

Gerronema lapidescens (Lei Wan), a valued medicinal basidiomycete traditionally employed for antiparasitic and digestive ailments, faces severe conservation threats due to unsustainable wild harvesting and the absence of reliable cultivation protocols. To address this crisis and unlock its pharmacotherapeutic potential, we present the first chromosome-scale genome assembly and comprehensive methylome profile for the wild strain G. lapidescens QL01, domesticated from the Qinling Mountains. A multi-platform sequencing strategy (Illumina and PacBio HiFi) yielded a high-quality 82.23 Mb assembly anchored to 11 chromosomes, exhibiting high completeness (98.4% BUSCO) and 46.03% GC content. Annotation predicted 15,847 protein-coding genes, with 81.12% functionally assigned. Genome-wide analysis identified 8.46 million high-confidence single-nucleotide polymorphisms (SNPs). Notably, methylation profiling revealed 3.25 million methylation events, with elevated densities on chromosomes 4, 9, and 10, suggesting roles in gene silencing and environmental adaptation. Phylogenomic analyses clarified the evolutionary status of G. lapidescens, whilst gene family evolution indicated moderate dynamics reflecting niche adaptation. Carbohydrate-Active enzymes (CAZymes) analysis identified 521 enzymes, including 211 Glycoside Hydrolases (GHs), consistent with organic matter degradation. Additionally, 3279 SSRs were catalogued as molecular markers. This foundational resource elucidates G. lapidescens’s genetic architecture, epigenetic regulation, evolutionary history, and enzymatic toolkit, underpinning future research into medicinal compound biosynthesis, environmental adaptation, germplasm conservation, and sustainable cultivation.

Medicinal fungi, due to their high nutritional and medicinal value along with safety, are regarded as invaluable resources for the discovery of new pharmaceuticals. Naematelia aurantialba, commonly known as the golden ear mushroom, is a rare medicinal and edible fungus in China, renowned for its rich nutritional profile and safety for consumption. It has a long-standing history of use in traditional medicine, with ancient texts frequently citing its benefits for liver protection and its efficacy in alleviating cough and phlegm. Modern pharmacological studies have revealed that the N. aurantialba contains various bioactive compounds and nutritional constituents, exhibiting multiple pharmacological activities, including hypoglycemic, lipid-lowering, immunomodulatory, antioxidant, antitumor, and anticoagulant effects. This review synthesizes the current literature on the active components, medicinal and nutritional values, and the cultivation history of this species, aiming to provide a reference for the rational development of N. aurantialba in health food and medical fields.

Sarcomyxa edulis is a characteristic low-temperature, edible mushroom in Northeast China. It has a delicious taste and rich nutritional and medicinal value. S. edulis can undergo explosive fruiting, neat fruiting, and unified harvesting, making it suitable for factory production. The molecular mechanisms underlying fruiting body development in S. edulis remain poorly understood. This study employed transcriptome analysis to compare the post-ripening mycelium (NPM) and primordial fruiting bodies (PRMs) of the thermostable S. edulis strain PQ650759, which uniquely forms primordia under constant temperature. A total of 4862 differentially expressed genes (DEGs) (|log2(fold change)| ≥ 1) were identified and found to be predominantly enriched in biological processes such as cell wall organization, DNA replication, and carbohydrate metabolism. KEGG pathway analysis revealed significant enrichment in 20 metabolic pathways, including mismatch repair, yeast cell cycle, and starch/sucrose metabolism. Ten candidate genes (e.g., SKP1, MRE11, GPI) linked to cell cycle regulation, DNA repair, and energy metabolism were randomly selected and prioritized for functional analysis. Quantitative PCR validation confirmed the reliability of transcriptome data, with expression trends consistent across both methods. Our findings provide critical insights into the molecular regulation of fruiting body development in S. edulis and establish a foundation for future mechanistic studies and strain optimization in industrial cultivation.