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Edible and Medicinal Macrofungi, 4th Edition
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Edible and Medicinal Macrofungi, 4th Edition

A special issue of Journal of Fungi (ISSN 2309-608X).

Deadline for manuscript submissions: 31 May 2026 | Viewed by 19779

Special Issue Editors

Prof. Dr. Ruilin Zhao

E-Mail Website
Guest Editor
State Key Laboratory of Mycology, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
Interests: diversity and systematics of macrofungi; evolutionary genomics; molecular biology of mushrooms
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Ling Liu

E-Mail Website
Guest Editor
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
Interests: fungal secondary metabolites; marine natural products; drug discovery; genome mining; biosynthesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Fungi with large fruiting bodies that can be identified by the naked eye are generally referred to as macrofungi. Taxonomically, most macrofungi species come from the Basidiomycota division and a few come from Ascomycota, and, up to now, around 40,000 species have been described. Macrofungi are closely related to economic activities. Humans have a long history of using macrofungi for food and medicine. A fungus is a “natural chemical factory”; with the deepening of fungus-related research, a large number of species and new active components have been found, and fungi have become one of the innovative powers at work in drugs and health products, especially with the development of biochemistry, enzyme engineering, genetic engineering, and macrofungi in food, medicine, and other areas, which show their wide-ranging prospects. In this Special Issue, we will provide a platform for the advances being made in our understanding of the biodiversity, resource, evolution, biology, and biochemistry of edible and medicinal macrofungi (EMM).

This Special Issue will cover, but is not limited to, content focused on the following:

  • The taxonomy and diversity of EMM;
  • The phylogeny, phylogeography, and evolution of EMM;
  • The molecular biology of EMM;
  • The bioactive compounds of EMM.

Prof. Dr. Ruilin Zhao
Dr. Ling Liu
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • mushroom
  • evolution
  • phylogeny
  • biology
  • bioactive compound

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Related Special Issues

Published Papers (8 papers)

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Research

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14 pages, 3767 KB  
Article
Genetic Diversity and Gene Flow of the Ectomycorrhizal Mushroom Lactarius hatsudake in Southern China: Evidence from SSR Markers
by Shatong Yang, Mingwei Mao, Jieyu Huang, Bing Gu and Kuan Zhao
J. Fungi 2026, 12(4), 280; https://doi.org/10.3390/jof12040280 - 15 Apr 2026
Viewed by 391
Abstract
Lactarius hatsudake is an ecologically and economically significant wild edible mushroom in southern China. To elucidate its population genetic diversity, differentiation, and evolutionary history, we analyzed 172 fruiting bodies from eight geographic populations (AQ, BS, DZ, JS, NC, PT, SG, YX) across seven [...] Read more.
Lactarius hatsudake is an ecologically and economically significant wild edible mushroom in southern China. To elucidate its population genetic diversity, differentiation, and evolutionary history, we analyzed 172 fruiting bodies from eight geographic populations (AQ, BS, DZ, JS, NC, PT, SG, YX) across seven provinces in the western and eastern regions of southern China using five highly polymorphic simple sequence repeat (SSR) markers. Combined with STRUCTURE clustering, discriminant analysis of principal components (DAPC), unweighted pair group method with arithmetic mean (UPGMA), and analysis of molecular variance (AMOVA), the results revealed high polymorphism across the studied loci (mean PIC = 0.842). A total of 75 alleles were identified, averaging 15 alleles per locus. At the population level, the mean effective number of alleles (Ne) was 4.023, and the mean unbiased gene diversity (uH) was 0.768. The NC population exhibited the highest genetic diversity (uH = 0.796), whereas the BS population showed relatively lower diversity (uH = 0.647). Clustering analyses (STRUCTURE, DAPC, and UPGMA) consistently identified two distinct genetic clusters (K = 2). Cluster I consisted of populations AQ, PT, BS, and SG, while Cluster II was composed of the remaining four populations. Notably, individuals from AQ and NC displayed significant genetic admixture, suggesting a transitional zone. AMOVA revealed that the majority of genetic variation (83%) resided within populations and 17% among populations. Moderate population differentiation (ENA-corrected global Fst = 0.102) and admixture signals suggest non-negligible connectivity among populations. Full article
(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)
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23 pages, 24193 KB  
Article
Unveiling Transcriptional Dynamics Across Five Developmental Stages of the Edible Mushroom Oudemansiella raphanipes
by Yanjun Ma, Lanlan Yu, Jinming Zhang, Yongxiang Dang and Xuetai Zhu
J. Fungi 2026, 12(2), 124; https://doi.org/10.3390/jof12020124 - 10 Feb 2026
Viewed by 801
Abstract
Oudemansiella raphanipes is a prized edible mushroom renowned for its “three-high, one-low” nutritional profile (high protein, fiber, vitamins; low fat). However, the stage-specific molecular dynamics governing its development and their potential link to its superior nutrition remain unknown, hindering targeted genetic improvement. This [...] Read more.
Oudemansiella raphanipes is a prized edible mushroom renowned for its “three-high, one-low” nutritional profile (high protein, fiber, vitamins; low fat). However, the stage-specific molecular dynamics governing its development and their potential link to its superior nutrition remain unknown, hindering targeted genetic improvement. This study aimed to decipher the first comprehensive transcriptomic atlas across its five key developmental stages and to explore potential molecular signatures linked to its distinctive nutrition. We first confirmed the superior nutritional profile of O. raphanipes via comparative analysis with nine commercial mushrooms. RNA sequencing (RNA-seq) was performed on samples from five defined developmental stages (spores, mycelia, primordia, closed-cap and open-cap fruiting bodies), followed by de novo transcriptome assembly, functional annotation, and differential expression analysis. Results revealed extensive transcriptional reprogramming, with the most dramatic changes occurring at the spore-to-mycelium transition (19,827 differentially expressed genes). Stage-specific pathway enrichment highlighted regulators of germination (e.g., ribosome, transmembrane transport), primordium formation (e.g., glycerophospholipid metabolism, GTPase signaling), fruiting body development (e.g., starch/sucrose metabolism, terpenoid synthesis), and maturation (e.g., glycolysis, fatty acid biosynthesis, transcription factors MADS-box/bZIP). We identified 588 stage-exclusive genes in spores and 515 constitutively upregulated genes linked to energy metabolism and proteostasis. Crucially, integrating nutritional phenotypes with stage-resolved transcriptomics revealed that sustained transcriptional programs in mature fruiting bodies are associated with its nutritional excellence; e.g., upregulation of ribosomal/amino acid metabolic pathways aligns with high protein content, while active fatty acid degradation correlates with low fat levels. Our study provides the first multi-stage transcriptomic blueprint for O. raphanipes development, revealing stage-specific regulators and proposing molecular associations for its nutritional traits. This resource offers a foundational basis and candidate genetic targets for future breeding strategies aimed at enhancing agronomic and nutritional traits in this prized fungus. Full article
(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)
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23 pages, 3256 KB  
Article
Genetic–Geographic–Chemical Framework of Polyporus umbellatus Reveals Lineage-Specific Chemotypes for Elite Medicinal Line Breeding
by Youyan Liu, Shoujian Li, Liu Liu, Bing Li and Shunxing Guo
J. Fungi 2026, 12(1), 39; https://doi.org/10.3390/jof12010039 - 3 Jan 2026
Viewed by 760
Abstract
Polyporus umbellatus is a valuable fungus with both dietary and medicinal applications. However, heterogeneous germplasm and chemical variability constrain its sustainable use. To elucidate the drivers of this variation, whole-genome resequencing and metabolic profiling were integrated. Genome-wide analysis of representative accessions revealed six [...] Read more.
Polyporus umbellatus is a valuable fungus with both dietary and medicinal applications. However, heterogeneous germplasm and chemical variability constrain its sustainable use. To elucidate the drivers of this variation, whole-genome resequencing and metabolic profiling were integrated. Genome-wide analysis of representative accessions revealed six distinct genetic clusters across China, identifying the Qinling–Daba Mountains as a putative center of diversity. Population analysis indicated severe genetic erosion with significant heterozygote deficits, likely driven by inbreeding and long-term clonal propagation. Multivariate analysis demonstrated that genetic lineage, rather than traditional commercial morphotypes (Zhushiling and Jishiling), is the primary determinant of metabolite accumulation. Specific lineages were identified as superior germplasm candidates: Group 2 consistently exhibited the highest genetic potential for accumulating steroids, whereas Group 4 attained the highest polysaccharide yield. Although the global genetic–chemical correlation was weak, implying environmental plasticity, the distinct clustering of superior lineages confirms that core accumulation patterns are genetically canalized. These findings advocate for shifting quality control from morphological grading to molecular-assisted selection. Ultimately, this framework provides an evidence-based foundation for urgent in situ conservation to restore genetic diversity and facilitates precision breeding of high-efficacy cultivars. Full article
(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)
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24 pages, 8271 KB  
Article
Combined Transcriptomic and Metabolomic Analyses of the Response of Ganoderma lucidum to Elevated CO2
by Tingting Fang, Lu Chen, Hui Yao, Ye Li, Guohui Liu, Shaofeng Wu, Jin Lan and Xiangdong Chen
J. Fungi 2026, 12(1), 5; https://doi.org/10.3390/jof12010005 - 20 Dec 2025
Cited by 2 | Viewed by 1201
Abstract
Carbon dioxide (CO2) is a key environmental factor that regulates the morphology of fruiting bodies in edible fungi. High CO2 concentrations often lead to the formation of antler-shaped abnormal fruiting bodies in Ganoderma lucidum. Yet, the molecular response mechanisms [...] Read more.
Carbon dioxide (CO2) is a key environmental factor that regulates the morphology of fruiting bodies in edible fungi. High CO2 concentrations often lead to the formation of antler-shaped abnormal fruiting bodies in Ganoderma lucidum. Yet, the molecular response mechanisms underlying this process remain unclear. To address this gap, this study integrated transcriptomics and untargeted metabolomics to compare the transcriptional and metabolic profiles of G. lucidum fruiting bodies at three growth stages, cultivated under both normal (0.04%) and high CO2 concentrations (0.3%). Metabolomic analysis revealed that, compared to the control groups, 387, 337, and 445 differentially accumulated metabolites were identified in the elevated-CO2 groups, respectively. Moreover, high CO2 concentrations led to a widespread down-regulation of various amino acids biosynthesis, accompanied by a marked accumulation of specific triterpenoids and steroids. This indicates distinct metabolite accumulation patterns in the fruiting bodies of G. lucidum cultivated under elevated CO2. Furthermore, transcriptomic analysis showed that, at a key stage of fruiting body development, high CO2 concentrations adversely affected gene expression of cell cycle-yeast, proteasome, DNA replication, mismatch repair, and meiosis-yeast pathways, which may decrease the cell division ability and prevent normal pileus development. Meanwhile, the differential expression of genes related to CO2 signal perception and transduction and cell wall remodeling provided a molecular basis for the morphogenesis of the antler-type fruiting bodies. Overall, this study delineates a multi-layered, multi-pathway regulatory network through which high CO2 concentrations affect the development and metabolism of G. lucidum, encompassing energy metabolism reprogramming, inhibition of cell division, and cell wall remodeling. This provides new insights into CO2 as an environmental signal in fungal development and a theoretical basis for optimizing G. lucidum cultivation practices. Full article
(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)
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26 pages, 914 KB  
Article
Species Diversity and Resource Status of Macrofungi in Beijing: Insights from Natural and Urban Habitats
by Dong-Mei Liu, Shi-Hui Wang, Ke Wang, Jia-Xin Li, Wen-Qiang Yang, Xi-Xi Han, Bin Cao, Shuang-Hui He, Wei-Wei Liu and Rui-Lin Zhao
J. Fungi 2025, 11(8), 607; https://doi.org/10.3390/jof11080607 - 21 Aug 2025
Cited by 1 | Viewed by 2691
Abstract
This study systematically documented macrofungal diversity in Beijing, China (field surveys conducted from 2020 to 2024) using line-transect and random sampling. A total of 1056 species were identified, spanning 2 phyla, 7 classes, 25 orders, 109 families, and 286 genera. The inventory includes [...] Read more.
This study systematically documented macrofungal diversity in Beijing, China (field surveys conducted from 2020 to 2024) using line-transect and random sampling. A total of 1056 species were identified, spanning 2 phyla, 7 classes, 25 orders, 109 families, and 286 genera. The inventory includes 12 new species, 456 new records for Beijing, 79 new records for China, and comprises 116 edible, 56 edible–medicinal, 123 medicinal, and 58 poisonous species. Among these, 542 species were assessed against China’s Macrofungi Redlist, revealing eight species needing conservation attention (seven Near Threatened, one Vulnerable). Analysis revealed stark differences in dominant taxa between natural ecosystems (protected areas) and urban green spaces/parks. In natural areas, macrofungi are dominated by 31 families (e.g., Russulaceae, Cortinariaceae) and 47 genera (e.g., Russula, Cortinarius). Ectomycorrhizal lineages prevailed, highlighting their critical role in forest nutrient cycling, plant symbiosis, and ecosystem integrity. In urban areas, 10 families (e.g., Agaricaceae, Psathyrellaceae) and 17 genera (e.g., Leucocoprinus, Coprinellus) were dominant. Saprotrophic genera dominated, indicating their adaptation to decomposing organic matter in human-modified habitats and the provision of ecosystem services. The study demonstrates relatively high macrofungal diversity in Beijing. The distinct functional guild composition—ectomycorrhizal dominance in natural areas versus saprotrophic prevalence in urban zones—reveals complementary ecosystem functions and underscores the conservation value of protected habitats for maintaining vital mycorrhizal networks. These findings provide fundamental data and scientific support for regional biodiversity conservation and sustainable macrofungal resource development. Full article
(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)
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15 pages, 2357 KB  
Article
Dynamics of Nutrient Components and Microbial Communities in Substrates During the Development of the Fruiting Bodies of Volvariella volvacea
by Le Wang, Qin Dong, Qian Guo, Lei Zha, Lin Yang, Changxia Yu and Yan Zhao
J. Fungi 2025, 11(7), 479; https://doi.org/10.3390/jof11070479 - 24 Jun 2025
Cited by 3 | Viewed by 2245
Abstract
Cotton waste, a growth medium for Volvariella volvacea, has significant commercial and nutritional value. Under controlled environmental conditions, substrate nutrient composition and microorganisms affect the growth of V. volvacea. In this study, the changes in the nutrient content of the substrate [...] Read more.
Cotton waste, a growth medium for Volvariella volvacea, has significant commercial and nutritional value. Under controlled environmental conditions, substrate nutrient composition and microorganisms affect the growth of V. volvacea. In this study, the changes in the nutrient content of the substrate at different stages of fruiting body development were compared based on an 86% waste cotton substrate, and microbial diversity was studied via 16S rRNA analysis. The results indicated that there were significant differences in nutrient content in the substrate at different stages of fruiting body development. The total contents of carbon, nitrogen, and phosphorus initially increased but then decreased due to nutrient absorption and utilization by V. volvacea. It was also found that large amounts of organic nitrogen decomposed into more readily utilizable inorganic nitrogen. The nutritional content and microbial community structure of the substrate during the egg stage significantly differed from those during the other four stages, making the egg stage the most critical period in cultivation. Through correlation analysis between nutrient content and microbial differences, it was found that differential microbial taxa (Beijerinckiaceae, Burkholderiales, Chitinophaga jiangningensis, etc.) with nitrogen fixation, denitrification, and cellulose decomposition functions were significantly related to carbon- and nitrogen-related indicators such as nitrate nitrogen, microbial biomass carbon, and alkali-hydrolyzed nitrogen. These microorganisms play important roles in determining the variation in the nutritional profile of the substrate. This study provides a theoretical basis for promoting the absorption and utilization of nutrients by V. volvacea by altering the structure of the microbial community of the growth substrate. Full article
(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)
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25 pages, 18127 KB  
Article
Mycelium Growth and Development of Psilocybe spp. Mother Cultures on Agar-Based Media
by Marco Pepe, Mohsen Hesami, Livia Fleishmann, Tom Hsiang and Andrew Maxwell Phineas Jones
J. Fungi 2025, 11(6), 450; https://doi.org/10.3390/jof11060450 - 13 Jun 2025
Cited by 1 | Viewed by 5570
Abstract
The resurgence of interest in the therapeutic potential of psilocybin-producing mushrooms has recently led to numerous research and commercialization efforts. Due to its ease of cultivation and high potency, Psilocybe is the primary genus of interest, and there is a growing need to [...] Read more.
The resurgence of interest in the therapeutic potential of psilocybin-producing mushrooms has recently led to numerous research and commercialization efforts. Due to its ease of cultivation and high potency, Psilocybe is the primary genus of interest, and there is a growing need to standardize maintenance, proliferation, and cultivation techniques for efficient and consistent production. The investigation of mycelial growth and development on agar-based media is of principal importance to regulate and optimize mycelium growth and preservation protocols for subsequent fruiting body development. The current investigation is the first to examine the mycelial growth and morphology of four Psilocybe genotypes cultured on different agar-based media. The results from this simple set of experiments provides the foundation for future optimization studies. Ultimately, the information presented can be used to develop genotype-specific mycelial growth and development practices that will shape the future of psychedelic mushroom production for clinical and industrial applications. Full article
(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)
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Review

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32 pages, 5250 KB  
Review
Artificial Intelligence in Edible Mushroom Cultivation, Breeding, and Classification: A Comprehensive Review
by Muharagi Samwel Jacob, Anran Xu, Keqing Qian, Zhengxiang Qi, Xiao Li and Bo Zhang
J. Fungi 2025, 11(11), 758; https://doi.org/10.3390/jof11110758 - 22 Oct 2025
Cited by 4 | Viewed by 5160
Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)
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