Search Results (45)

Cyclocybe chaxingu is a well-known edible fungus in China, in which pileus size and color are key traits determining its commercial value. However, the molecular genetic mechanisms underlying the morphological development of its pileus remains limited at present. To address this, our study first completed the high-quality genome assembly of the monokaryotic strain Ag.c0002-1 of albino C. chaxingu, anchoring it to 13 chromosomes via Hi-C technology. The final genome size was 51.7 Mb with a GC content of 51.06%, and 11,332 protein-coding genes were annotated. Phenotypic observations and comparative transcriptome analyses were then conducted on the pilei of the brown cultivar Ag.c0067 and the white cultivar Ag.c0002 at the primordium, elongation, and mature stages. Phenotypic analysis revealed continuous pileus expansion accompanied by progressive color lightening in both cultivars during development. Comparative transcriptomic analyses revealed significant differences in gene expression patterns between the two cultivars across developmental stages. KEGG enrichment analysis indicated that pileus expansion is closely associated with pathways related to DNA replication, cell cycle of yeast, carbon metabolism, and carbohydrate digestion and absorption. Among these, differentially expressed genes involved in cell division tended to be downregulated, whereas genes associated with energy metabolism and substance transport were upregulated, providing the necessary energy and material support for pileus growth. Changes in pileus pigmentation were primarily associated with tyrosine metabolism, betalain biosynthesis, tryptophan metabolism, and melanogenesis pathways. Notably, the downregulation of tyrosinase genes and the upregulation of glutathione S-transferase genes during development may represent major molecular mechanisms underlying pileus color lightening. Overall, this study provides important insights into the molecular mechanisms regulating pileus development and pigmentation in C. chaxingu, while also offering valuable theoretical support for genetic analysis of basidiomycete morphogenesis and the molecular breeding of edible mushrooms. Full article

Estimating the mass of Oudemansiella raphanipies quickly and accurately is indispensable in optimizing post-harvest packaging processes. Traditional methods typically involve manual grading followed by weighing with a balance, which is inefficient and labor-intensive. To address the challenges encountered in actual production scenarios, in this work, we developed a novel pipeline for estimating the mass of multiple Oudemansiella raphanipies. To achieve this goal, an enhanced deep learning (DL) algorithm for instance segmentation and a machine learning (ML) model for mass prediction were introduced. On one hand, to segment multiple samples in the same image, a novel instance segmentation network named FinePoint-ORSeg was applied to obtain the finer edges of samples, by integrating an edge attention module to improve the fineness of the edges. On the other hand, for individual samples, a novel cap–stem segmentation approach was applied and 18 phenotypic parameters were obtained. Furthermore, principal component analysis (PCA) was utilized to reduce the redundancy among features. Combining the two aspects mentioned above, the mass was computed by an exponential GPR model with seven principal components. In terms of segmentation performance, our model outperforms the original Mask R-CNN; the $\mathrm{A}\mathrm{P}$, ${\mathrm{A}\mathrm{P}}_{50}$, ${\mathrm{A}\mathrm{P}}_{75}$, and ${\mathrm{A}\mathrm{P}}_{\mathrm{s}}$ are improved by 2%, 0.7%, 1.9%, and 0.3%, respectively. Additionally, our model outperforms other networks such as YOLACT, SOLOV2, and Mask R-CNN with Swin. As for mass estimation, the results show that the average coefficient of variation (CV) of a single sample mass in different attitudes is 6.81%. Moreover, the average mean absolute percentage error (MAPE) for multiple samples is 8.53%. Overall, the experimental results indicate that the proposed method is time-saving, non-destructive, and accurate. This can provide a reference for research on post-harvest packaging technology for Oudemansiella raphanipies. Full article

Rhodotus palmatus is commercially marketed as ‘fruity-scented mushroom’, a novel cultivar first brought into commercial cultivation in China at the end of 2023. It is characterized by a distinct pinkish pigmentation, a pileus with a distinct reticulated surface pattern, and an intense fruity aroma. To date, only a few natural strains have been documented in China, and scientific research on this species remains scarce. This study successfully bred a new variety of Rhodotus palmatus and established corresponding efficient techniques for its industrial-scale cultivation. As a result, strain ZJGWG001, known for its short growth cycle (23 d), high yield potential (177.43 ± 10.08 g·bag⁻¹) and biological efficiency (59.1%), and distinctive, stable phenotypic traits, is well suited for industrial cultivation. This cultivar is the first newly registered Rhodotus palmatus variety in China to receive provincial-level certification and has been officially designated as ‘Zhongjunguoweigu No. 1’. It represents an important discovery in the collection and exploration of wild fungal germplasm resources in recent years. Full article

Core germplasm, a strategically selected subset of the original germplasm, aims to maximize the representation of genetic diversity within the entire collection. Establishing a germplasm resource bank is essential for the effective management and sustainable utilization of genetic resources. This study developed a core germplasm repository for Hypsizygus marmoreus, a commercially important mushroom species, to capture the genetic diversity of the original collection with a minimal sample size. Genetic diversity and cluster analyses were conducted on 57 representative strains of H. marmoreus, including both cultivated and wild accessions from different regions, using 15 pairs of simple sequence repeat (SSR) markers. DNA molecular identity cards were generated for all germplasms, and cultivation trials with agronomic trait assessments were performed on 24 core accessions. A total of 115 distinct alleles were identified, with genetic similarity coefficients ranging from 0.70 to 1.00. Clustering at a similarity threshold of 0.76 classified the strains into five groups. The core germplasm panel, comprising 24 accessions (42.11% of the total collection), retained full allelic diversity and preserved the genetic and phenotypic variability of the original population, confirming its suitability for parental selection in breeding programs. unique molecular identity codes were developed for each H. marmoreus germplasm by integrating SSR marker profiles with data on geographical origin, fruiting body color, and cultivation traits. These were converted into DNA molecular ID codes, providing a reliable system for rapid identification and traceability of germplasm resources. The findings offer a valuable reference for breeding improvement and the protection of edible fungal varieties with independent intellectual property rights. Full article

Plant-based meat (PBM) products have rapidly grown in popularity due to increasing consumer demand for sustainable, ethical, and health-oriented food alternatives. However, these novel products may pose microbiological risks similar to traditional meats, including contamination by Salmonella spp. In this study, PBM samples (n = 63), including raw products (ground pork, mushroom, and burger) and cooked products (chicken tender, chicken breast, nugget, and beef), were collected from local retail markets in Bangkok, Thailand. The prevalence of Salmonella spp. was assessed by calculating the proportion of confirmed positive samples relative to the total number of PBM products tested. Additionally, the genomic characteristics and antibiotic susceptibility of Salmonella isolated from PBM were also investigated. From the result, Salmonella enterica was detected in 2.44% (1/41) of raw PBM samples, whereas no contamination was observed in cooked PBM products (0/22). Serovar identification revealed the isolate to be S. Anatum. Whole genome sequencing (WGS) analysis revealed the genome of S. Anatum SPBM3 consisted of 4,726,256 base pairs with 52.15% GC content, encoding 4717 coding sequences (CDS). Pangenomic analyses placed S. Anatum SPBM3 within a distinct sub-cluster closely related to pathogenic Salmonella strains previously reported, confirming its identity as part of the S. enterica lineage. The genome harbored 67 antimicrobial resistance genes, 5 prophage elements, and 305 key virulence determinants. Phenotypically, the isolate exhibited susceptibility to most tested antibiotics but showed intermediate resistance to streptomycin, ciprofloxacin, and colistin. Our findings highlight the potential microbial risks associated with PBM products and emphasize the importance of genomic surveillance to ensure food safety and public health protection as dietary preferences evolve toward non-traditional food matrices. Full article

Edible mushrooms have gained global popularity due to their nutritional value, medicinal properties, bioactive compounds and industrial applications. Despite their long-standing roles in ecology, nutrition, and traditional medicine, their additional functions in cultivation, breeding, and classification processes are still in their infancy due to technological constraints. The advent of Artificial Intelligence (AI) technologies has transformed the cultivation process of mushrooms, genetic breeding, and classification methods. However, the analysis of the application of AI in the mushroom production cycle is currently scattered and unorganized. This comprehensive review explores the application of AI technologies in mushroom cultivation, breeding, and classification. Four databases (Scopus, IEEE Xplore, Web of Science, and PubMed) and one search engine (Google Scholar) were used to perform a thorough review of the literature on the utility of AI in various aspects of the mushroom production cycle, including intelligent environmental control, disease detection, yield prediction, germplasm characterization, genotype–phenotype integration, genome editing, gene mining, multi-omics, automatic species identification and grading. In order to fully realize the potential of these edge-cutting AI technologies in transforming mushroom breeding, classification, and cultivation, this review addresses challenges and future perspectives while calling for interdisciplinary approaches and multimodal fusion. Full article

Edible mushrooms are increasingly recognized for their high nutritional value and contribution to a healthy diet. Among them, Agaricus bisporus is the most commercially important species in Europe and North America. However, the environmental impact of traditional peat use in A. bisporus cultivation necessitates the development of sustainable alternatives, given the ecological significance of peatlands. When evaluating casing materials, it is essential to consider not only yield but also other critical factors influencing marketability, such as nutritional value, appearance, and texture. This systematic review examines seventeen studies published between 1989 and 2025 that investigated various peat substitutes while assessing a range of quality criteria. The findings were categorized into seven groups, encompassing both chemical composition and phenotypic characteristics of the fruiting bodies. Most studies focused on the organic and inorganic content of the fruiting bodies, followed by measurements of size and weight. Some alternative casings, for example, increased dry matter contents, which indicates a high solid substance content, such as of proteins or minerals. However, this was not always beneficial, as it could negatively affect texture. Overall, the reviewed studies demonstrate that different casing materials can directly influence quality parameters, and even minor adjustments in casing composition can enhance fruiting body quality. Full article

Phenotypic traits of fungi and their automated extraction are crucial for evaluating genetic diversity, breeding new varieties, and estimating yield. However, research on the high-throughput, rapid, and non-destructive extraction of fungal phenotypic traits using 3D point clouds remains limited. In this study, a smart phone is used to capture multi-view images of shiitake mushrooms (Lentinula edodes) from three different heights and angles, employing the YOLOv8x model to segment the primary image regions. The segmented images were reconstructed in 3D using Structure from Motion (SfM) and Multi-View Stereo (MVS). To automatically segment individual mushroom instances, we developed a CP-PointNet++ network integrated with clustering methods, achieving an overall accuracy (OA) of 97.45% in segmentation. The computed phenotype correlated strongly with manual measurements, yielding R² > 0.8 and nRMSE < 0.09 for the pileus transverse and longitudinal diameters, R² = 0.53 and RMSE = 3.26 mm for the pileus height, R² = 0.79 and nRMSE = 0.12 for stipe diameter, and R² = 0.65 and RMSE = 4.98 mm for the stipe height. Using these parameters, yield estimation was performed using PLSR, SVR, RF, and GRNN machine learning models, with GRNN demonstrating superior performance (R² = 0.91). This approach was also adaptable for extracting phenotypic traits of other fungi, providing valuable support for fungal breeding initiatives. Full article

Psilocybe cubensis, a widely recognized psychoactive mushroom species, has played a significant role in both historical and modern therapeutic practices. This review explores the complex interplay between genetic diversity, strain variability and environmental factors that shape the biosynthesis of key psychoactive compounds, including psilocybin and psilocin. With many strains exhibiting substantial variability in their phenotypic characteristics and biochemical content, understanding and documenting this diversity is crucial for optimizing therapeutic applications. The review also highlights advances in cultivation techniques, such as submerged fermentation of the mycelium, and innovative analytical methodologies that have improved the precision of compound quantification and extraction. Although there is limited scientific information on P. cubensis due to nearly four decades of regulatory restrictions on psychedelic research, recent developments in genetic and biochemical studies are beginning to provide valuable insights into its therapeutic potential. Furthermore, this review emphasizes key knowledge gaps and offers insights into future research directions to advance the cultivation, scientific documentation of strain diversity, regulatory considerations and therapeutic use of P. cubensis. Full article

Termitomyces mushrooms, known for their symbiotic relationship with termites and their high nutritional and medicinal value, are challenging to cultivate artificially due to their specific growth requirements. This study investigates the impact of arginine on the mycelial growth, development, and lignocellulolytic capabilities of Termitomyces. We found that arginine significantly promoted conidia formation, altered mycelial morphology, and enhanced biomass and polysaccharide content. The addition of arginine also upregulated the expression of the enzymes related to lignocellulose decomposition, leading to increased activities of cellulase, hemicellulase, and laccase, which accelerated the decomposition and utilization of corn straw. A transcriptome analysis revealed differential expression patterns of carbohydrate-active enzyme genes in arginine-supplemented Termitomyces mycelia, providing insights into the molecular mechanisms underlying these enhancements. The GO enrichment analysis and KEGG pathway analysis highlighted the role of arginine in transmembrane transport, fatty acid oxidation, and carbohydrate metabolism. This study offers a molecular basis for the observed phenotypic changes and valuable insights for developing optimal culture strategies for Termitomyces, potentially enhancing its artificial cultivation and application in the bioconversion of lignocellulosic waste. Full article

Background: Strains XG04 and XGT2 of Lentinus edodes (Berk.) Singer demonstrate a high degree of genomic similarity, with XGT2 representing a systematic selection of XG04 and exhibiting enhanced phenotypic traits. Methods: An investigation into the differences between these strains was conducted using untargeted metabolomics to identify potential causal factors. Five exogenous inducers were assessed for their relationship with the observed phenotypes, and their impacts on fruiting body characteristics were analyzed. Results: Notably, the exogenous inducer rolipram, at a concentration of 0.4%, was found to increase cAMP expression levels in L. edodes primordia, which subsequently affected gill development, leading to the formation of gill-free fruiting bodies. Morphological differences between the two strains were evident; XG04 exhibited a spherical morphology with absent gills, rendering it commercially unviable, whereas XGT2 displayed a thicker cap and a more robust stipe, maintaining its characteristic umbrella shape. Conclusions: As the concentration of rolipram increased, both cap retraction and gill reduction in XGT2 occurred in a dose-dependent manner. The endogenous cAMP levels in the fruiting bodies were measured before and after rolipram treatment, revealing that the cap retraction and gill reduction in XGT2 progressed in a dose-dependent manner alongside increasing cAMP expression levels. Furthermore, a positive correlation was observed between cAMP levels and rolipram concentration. This study provides a foundation for improving the quality and productivity of mushroom cultivation by manipulating fruiting body characteristics through external stimuli. Full article

Biofilms are unique, multicellular life forms that challenge our understanding of the microbial functioning. The last decades of research on biofilms have allowed us to better understand their importance in the context of both health and various pathologies in the human body, although many knowledge gaps hindering their correct comprehension still exist. Biofilms are classically described as mushroom-shaped structures attached to the substrate; however, an increasing body of evidence shows that their morphology in clinical conditions may differ significantly from that classically presented. Although this may result partly from the unique physicochemical conditions within the host, the interaction between microbes and immune cells during development of a biofilm should not be underestimated. The current Opinion confronts the classical view on biofilms with the latest scientific research describing the vitality of interactions with immune cells as a modulator of the biofilm phenotype and behavior in clinical conditions. Full article

Beech mushrooms (Hypsizygus marmoreus) are edible mushrooms commercially used in South Korea. They can be classified into white and brown according to their pigmentation. This study analyzed the metabolites and biological activities of these mushrooms. Specifically, 42 metabolites (37 volatiles, two phenolics, and three carbohydrates) were quantified in white beech mushrooms, and 47 (42 volatiles, two phenolics, and three carbohydrates) were detected in brown mushrooms. The major volatiles detected were hexanal, pentanal, 1-hexanol, and 1-pentanol. Brown mushrooms contained higher levels of hexanal (64%) than white mushrooms (35%), whereas white mushrooms had higher levels of pentanal (11%) and 1-pentanol (3%). Most volatiles were more abundant in white mushrooms than in brown mushrooms. Furthermore, brown beech mushrooms had a higher phenolic content than white mushrooms. Biological assays revealed that both types of mushroom demonstrated anti-microbial activities against bacterial and yeast pathogens and weak DPPH scavenging activity. The extracts from both mushrooms (50 μg/mL) also exhibited strong anti-inflammatory properties. Brown mushroom extracts showed higher antioxidant, anti-microbial, and anti-inflammatory properties than white mushroom extracts. This study reported that the differences in phenotype, taste, and odor were consistent with the metabolite differences between white and brown beech mushrooms, which have high nutritional and biofunctional values. Full article

Mushroom cap is a key trait in the growth process and its phenotypic parameters are essential for automatic cultivation and smart breeding. However, the edible mushrooms are usually grown densely with mutual occlusion, which is difficult to obtain the phenotypic parameters non-destructively. Although deep learning methods achieve impressive performance with superior generalization capabilities, they require a large amount of ground truth label of the occluded target, which is a challenging task due to the substantial workload. To overcome this obstacle, a novel synthetic cap occlusion image method was proposed for rapidly generating edible mushroom occlusion datasets using raw images, in which the ground truth is obtained from the real world and the occlusion is randomly generated for simulating real scenes. Moreover, variants of amodal instance segmentation models with different backbone were trained and evaluated on our synthetic occlusion image datasets. Finally, an amodal mask-based size estimation method was presented to calculate the width and length of the cap. The experimental results showed that the amodal instance segmentation achieved an AP_@[0.5:0.95] of 82%, 93% and 96% on Oudemansiella raphanipes, Agrocybe cylindraceas and Pholiota nameko synthetic cap datasets, respectively, with a size of 1024 × 1024 px, which indicates that our occlusion image synthesis method can effectively simulate the real cap occlusion situation. The size estimation method achieved an $R^2$ of 0.95 and 0.98 between predictive amodal caps and manually labeled caps for the length and width of Agrocybe cylindraceas cap, respectively, which can be applied to obtain the phenotypic parameters of each cap effectively and accurately. These methods not only meet the demand for automatic monitoring of edible mushroom morphology in factories but also provide technical support for intelligent breeding. Full article

Chitosan is a derivative of chitin that is one of the most abundant biopolymers in nature, found in crustacean shells as well as in fungi cell walls. Most of the commercially available chitosans are produced from the exoskeletons of crustaceans. The extraction process involves harsh chemicals, has limited potential due to the seasonal and limited supply and could cause allergic reactions. However, chitosan has been shown to alleviate the negative effect of environmental stressors in plants, but there is sparse evidence of how chitosan source affects this bioactivity. The aim of this study was to investigate the ability of chitosan from mushroom in comparison to crustacean chitosan in enhancing drought stress tolerance in tomato plants (cv. MicroTom). Chitosan treatment was applied through foliar application and plants were exposed to two 14-day drought stress periods at vegetative and fruit set growth stages. Phenotypic (e.g., fruit number and weight), physiological (RWC) and biochemical-stress-related markers (osmolytes, photosynthetic pigments and malondialdehyde) were analyzed at different time points during the crop growth cycle. Our hypothesis was that this drought stress model will negatively impact tomato plants while the foliar application of chitosan extracted from either crustacean or mushroom will alleviate this effect. Our findings indicate that drought stress markedly decreased the leaf relative water content (RWC) and chlorophyll content, increased lipid peroxidation, and significantly reduced the average fruit number. Chitosan application, regardless of the source, improved these parameters and enhanced plant tolerance to drought stress. It provides a comparative study of the biostimulant activity of chitosan from diverse sources and suggests that chitosan sourced from fungi could serve as a more sustainable and environmentally friendly alternative to the current chitosan from crustaceans. Full article