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Molecular Biology of Mushroom
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Molecular Biology of Mushroom

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: 15 November 2025 | Viewed by 3947

Special Issue Editor

Dr. Young-Jin Park

E-Mail Website
Guest Editor
Department of Medicinal Biosciences, Research Institute for Biomedical & Health Science, College of Biomedical and Health Science, Konkuk University, 268 Chungwon-daero, Chungju-si 27478, Republic of Korea
Interests: fermentation; bioactive compounds; applied microbiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Mushrooms have long been used as food and medicinal ingredients and are an excellent model for biological research.  However, many mushrooms' basic biology and genetics are poorly understood. Fortunately, with the development of various molecular biology technologies, the biological properties of mushrooms that were not understood until now are gradually being revealed, and the various uses of mushrooms are attracting attention. Recently, Omics-based research on various mushrooms has been actively conducted, and the veil on mushrooms is gradually lifted. Through this, the biological characteristics of mushrooms and their genetic characteristics are being revealed. In addition, many mushrooms produce toxins, and their medical uses are also receiving attention. 

In this Special Issue, we invite you to participate in introducing the latest achievements in the field of molecular biology of mushrooms. This will not only be helpful to researchers in various fields researching mushrooms but will also contribute to the development of related research fields.

Dr. Young-Jin Park
Guest Editor

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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • molecular biology
  • genetics
  • genomics
  • transcriptomics
  • medicinal uses
  • metabolism and metabolites
  • evolution
  • fruiting body development
  • genome editing
  • phylogeny

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Published Papers (5 papers)

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Research

18 pages, 2432 KiB  
Article
High Carbon Dioxide Concentration Inhibits Pileus Growth of Flammulina velutipes by Downregulating Cyclin Gene Expression
by Kwan-Woo Lee, Che-Hwon Park, Seong-Chul Lee, Ju-Hyeon Shin and Young-Jin Park
J. Fungi 2025, 11(8), 551; https://doi.org/10.3390/jof11080551 - 24 Jul 2025
Viewed by 148
Abstract
Flammulina velutipes is a widely cultivated edible mushroom in East Asia, recognized for its nutritional benefits and distinct morphology characterized by a long stipe and a compact, hemispherical pileus. The pileus not only plays a critical biological role in reproduction through spore formation [...] Read more.
Flammulina velutipes is a widely cultivated edible mushroom in East Asia, recognized for its nutritional benefits and distinct morphology characterized by a long stipe and a compact, hemispherical pileus. The pileus not only plays a critical biological role in reproduction through spore formation but also serves as a key commercial trait influencing consumer preference and market value. Despite its economic importance, pileus development in F. velutipes is highly sensitive to environmental factors, among which carbon dioxide (CO2) concentration is particularly influential under indoor cultivation conditions. While previous studies have reported that elevated CO2 levels can inhibit pileus expansion in other mushroom species, the molecular mechanisms by which CO2 affects pileus growth in F. velutipes remain poorly understood. In this study, we investigated the impact of CO2 concentration on pileus morphology and gene expression in F. velutipes by cultivating fruiting bodies under two controlled atmospheric conditions: low (1000 ppm) and high (10,000 ppm) CO2. Morphometric analysis revealed that elevated CO2 levels significantly suppressed pileus expansion, reducing the average diameter by more than 50% compared to the low CO2 condition. To elucidate the underlying genetic response, we conducted RNA sequencing and identified 102 differentially expressed genes (DEGs), with 78 being downregulated under elevated CO2. Functional enrichment analysis highlighted the involvement of cyclin-dependent protein kinase regulatory pathways in this response. Two cyclin genes were found to be significantly downregulated under elevated CO2 conditions, and their suppression was validated through quantitative real-time PCR. These genes, possessing conserved cyclin_N domains, are implicated in the regulation of the eukaryotic cell cycle, particularly in mitotic growth. These results indicate that CO2-induced downregulation of cyclin genes may underlie cell cycle arrest, contributing to inhibited pileus development. This study is the first to provide transcriptomic evidence that elevated CO2 concentrations specifically repress PHO80-like cyclin genes in F. velutipes, revealing a molecular mechanism by which CO2 stress inhibits pileus development. These findings suggest that elevated CO2 triggers a morphogenetic checkpoint by repressing PHO80-like cyclins, thereby modulating cell cycle progression during fruiting body development. This study provides the first evidence of such a transcriptional response in edible mushrooms and offers promising molecular targets for breeding CO2-resilient strains and optimizing commercial cultivation conditions. Full article
(This article belongs to the Special Issue Molecular Biology of Mushroom)
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18 pages, 3361 KiB  
Article
Mechanism Underlying Ganoderma lucidum Polysaccharide Biosynthesis Regulation by the β-1,3-Glucosyltransferase Gene gl20535
by Jingyun Liu, Mengmeng Xu, Mengye Shen, Junxun Li, Lei Chen, Zhenghua Gu, Guiyang Shi and Zhongyang Ding
J. Fungi 2025, 11(7), 532; https://doi.org/10.3390/jof11070532 - 17 Jul 2025
Viewed by 406
Abstract
Ganoderma lucidum polysaccharides (GLPs) are natural compounds with a broad spectrum of biological activities. β-1,3-glucosyltransferase (GL20535) plays an important role in polysaccharide synthesis by catalyzing the transfer of UDP-glucose to extend sugar chains, but its underlying mechanism remains unclear. In this study, [...] Read more.
Ganoderma lucidum polysaccharides (GLPs) are natural compounds with a broad spectrum of biological activities. β-1,3-glucosyltransferase (GL20535) plays an important role in polysaccharide synthesis by catalyzing the transfer of UDP-glucose to extend sugar chains, but its underlying mechanism remains unclear. In this study, the regulatory mechanism of GL20535 in polysaccharide synthesis was elucidated by overexpressing and silencing gl20535 in G. lucidum. Overexpression of gl20535 resulted in maximum increases of 18.08%, 79.04%, and 18.01% in intracellular polysaccharide (IPS), extracellular polysaccharide (EPS), and β-1,3-glucan contents, respectively. In contrast, silencing gl20535 resulted in maximum reductions of 16.97%, 30.20%, and 23.56% in IPS, EPS, and β-1,3-glucan contents, respectively. These phenomena in the overexpression strains were attributed to gl20535-mediated promotion of UDP-glucose synthesis in the sugar donor pathway and upregulation of the expression of glycoside hydrolase genes. The opposite trend was observed in the silenced strains. In mycelial growth studies, neither overexpression nor silencing of gl20535 affected biomass and cell wall thickness. Furthermore, the GL20535 isozyme gene gl24465 remained unaffected in gl20535-overexpressed strains but was upregulated in gl20535-silenced strains, suggesting a compensatory regulatory relationship. These findings reveal the regulatory role of GL20535 on gene expression in the GLPs synthesis pathway and deepen our understanding of GL20535 function in the polysaccharide network of edible and medicinal fungi. Full article
(This article belongs to the Special Issue Molecular Biology of Mushroom)
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16 pages, 7281 KiB  
Article
Decoding the Tissue-Specific Profiles of Bioactive Compounds in Helvella leucopus Using Combined Transcriptomic and Metabolomic Approaches
by Qian Zhou, Xusheng Gao, Junxia Ma, Haoran Zhao, Dan Gao and Huixin Zhao
J. Fungi 2025, 11(3), 205; https://doi.org/10.3390/jof11030205 - 6 Mar 2025
Viewed by 878
Abstract
Helvella leucopus, an endangered wild edible fungus, is renowned for its distinct health benefits and nutritional profile, with notable differences in the bioactive and nutritional properties between its cap and stipe. To investigate the molecular basis of these tissue-specific variations, we conducted [...] Read more.
Helvella leucopus, an endangered wild edible fungus, is renowned for its distinct health benefits and nutritional profile, with notable differences in the bioactive and nutritional properties between its cap and stipe. To investigate the molecular basis of these tissue-specific variations, we conducted integrative transcriptomic and metabolomic analyses. Metabolomic profiling showed that the cap is particularly rich in bioactive compounds, including sterols and alkaloids, while the stipe is abundant in essential nutrients, such as glycerophospholipids and amino acids. Transcriptomic analysis revealed a higher expression of genes involved in sterol biosynthesis (ERG1, ERG3, ERG6) and energy metabolism (PGK1, ENO1, PYK1) in the cap, suggesting a more active metabolic profile in this tissue. Pathway enrichment analysis highlighted tissue-specific metabolic pathways, including riboflavin metabolism, pantothenate and CoA biosynthesis, and terpenoid backbone biosynthesis, as key contributors to the unique functional properties of the cap and stipe. A detailed biosynthetic pathway network further illustrated how these pathways contribute to the production of crucial bioactive and nutritional compounds, such as sterols, alkaloids, linoleic acid derivatives, glycerophospholipids, and amino acids, in each tissue. These findings provide significant insights into the molecular mechanisms behind the health-promoting properties of the cap and the nutritional richness of the stipe, offering a theoretical foundation for utilizing H. leucopus in functional food development and broadening our understanding of bioactive and nutritional distribution in edible fungi. Full article
(This article belongs to the Special Issue Molecular Biology of Mushroom)
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19 pages, 2969 KiB  
Article
Haplotype-Phased Chromosome-Level Genome Assembly of Cryptoporus qinlingensis, a Typical Traditional Chinese Medicine Fungus
by Yu Song, Ming Zhang, Yu-Ying Liu, Minglei Li, Xiuchao Xie and Jianzhao Qi
J. Fungi 2025, 11(2), 163; https://doi.org/10.3390/jof11020163 - 19 Feb 2025
Cited by 3 | Viewed by 945
Abstract
This study presents the first comprehensive genomic analysis of Cryptoporus qinlingensis, a classical folk medicine and newly identified macrofungus from the Qinling Mountains. Utilizing advanced sequencing technologies, including PacBio HiFi and Hi-C, we achieved a high-quality chromosome-level genome assembly. The genome, sized [...] Read more.
This study presents the first comprehensive genomic analysis of Cryptoporus qinlingensis, a classical folk medicine and newly identified macrofungus from the Qinling Mountains. Utilizing advanced sequencing technologies, including PacBio HiFi and Hi-C, we achieved a high-quality chromosome-level genome assembly. The genome, sized at 39.1 Mb, exhibits a heterozygosity of 0.21% and contains 21.2% repetitive sequences. Phylogenetic analysis revealed a recent divergence of C. qinlingensis from Dichomitus squalens approximately 212.26 million years ago (MYA), highlighting the rapid diversification within the Polyporaceae family. Comparative genomic studies indicate significant gene family contraction in C. qinlingensis, suggesting evolutionary adaptations. The identification of a tetrapolar mating system, along with the analysis of CAZymes and P450 genes, underscores the genomic complexity and ecological adaptability of this species. Furthermore, the discovery of 30 biosynthetic gene clusters (BGCs) related to secondary metabolites, including polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), and terpene synthesis enzymes, opens new avenues for exploring bioactive compounds with potential medicinal applications. This research not only enriches our understanding of the Cryptoporus genus but also provides a valuable foundation for future studies aiming to harness the therapeutic potential of C. qinlingensis and to further explore its ecological and evolutionary significance. Full article
(This article belongs to the Special Issue Molecular Biology of Mushroom)
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20 pages, 17936 KiB  
Article
Genome Sequencing Providing Molecular Evidence of Tetrapolar Mating System and Heterothallic Life Cycle for Edible and Medicinal Mushroom Polyporus umbellatus Fr.
by Shoujian Li, Youyan Liu, Liu Liu, Bing Li and Shunxing Guo
J. Fungi 2025, 11(1), 15; https://doi.org/10.3390/jof11010015 - 28 Dec 2024
Viewed by 1082
Abstract
Polyporus umbellatus is a species whose sclerotia have been extensively employed in traditional Chinese medicine, which has diuretic, antitumor, anticancer, and immune system enhancement properties. However, prolonged asexual reproduction has resulted in significant homogenization and degeneration of seed sclerotia. In contrast, sexual reproduction [...] Read more.
Polyporus umbellatus is a species whose sclerotia have been extensively employed in traditional Chinese medicine, which has diuretic, antitumor, anticancer, and immune system enhancement properties. However, prolonged asexual reproduction has resulted in significant homogenization and degeneration of seed sclerotia. In contrast, sexual reproduction has emerged as an effective strategy to address these challenges, with a distinct mating system serving as the foundation for the implementation of sexual breeding. This study presents the first sequencing and assembly of the genome of P. umbellatus, thereby providing an opportunity to investigate the mating system at the genomic level. Based on the annotated mating-type loci within the genome, monokaryotic offspring exhibiting different mating-types were identified. Through the integration of traditional mating tests, the tetrapolar mating system of P. umbellatus was distinctly elucidated. The resequencing of monokaryotic strains with four different mating-types, along with comparative analyses of mating-type loci, revealed the HD1 and HD2 (HD, homeodomain) genes determined the mating A types, and the PR4, PR5, and PR6 (PR, pheromone receptor) genes determined the mating B types. Meanwhile, this study offers a successful case study in the molecular investigation of mating systems. Additionally, the number of sterigma and basidiospores on each basidium was examined using scanning electron microscopy, while the nuclei of basidiospores and basidia at various developmental stages were analyzed through DAPI staining. This research clarifies the heterothallic life cycle of P. umbellatus. The findings of this study are expected to facilitate advancements in genetic research, breeding development, strain improvement, and the industry of P. umbellatus. Full article
(This article belongs to the Special Issue Molecular Biology of Mushroom)
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