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Molecular Biology of Mushroom, 2nd Edition

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A Special Issue of Journal of Fungi (ISSN 2309-608X) belonging to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 11315

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Dr. Young-Jin Park

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Department of Medicinal Biosciences, Konkuk University, Chungju 27478, Republic of Korea
Interests: genomics; transcriptomics; medicinal mushroom metabolite; epigenetics; cultivation; system biology
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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

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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-anonymized 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

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Related Special Issue

Molecular Biology of Mushroom in Journal of Fungi (7 articles)

Published Papers (8 papers)

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Research

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20 pages, 6212 KB

Open AccessArticle

Isolation and Anti-Melanogenic Activity of Polycarpol from Ganoderma lucidum Mycelia: Expanding the Functional Potential of Cultured Mycelial Biomass

by Che-Hwon Park, Sung-Chul Lee, Rae-Won Kang and Young-Jin Park

J. Fungi 2026, 12(8), 625; https://doi.org/10.3390/jof12080625 - 19 Aug 2026

Viewed by 457

Abstract

Ganoderma lucidum is a medicinal mushroom widely recognized as a source of bioactive metabolites, particularly triterpenoids. Although most studies have focused on fruiting bodies and spores, the potential of cultured mycelial biomass as a source of functional secondary metabolites remains less explored. In this study, we isolated and characterized polycarpol from the mycelia of G. lucidum and evaluated its anti-melanogenic activity in B16F10 murine melanoma cells. Dried mycelia obtained after liquid culture were extracted with 70% ethanol, partitioned with ethyl acetate, and purified by repeated chromatographic separation. The isolated compound was identified as polycarpol by LC–ESI–MS, HR-MS/MS, and NMR spectroscopy, together with comparison with previously reported spectroscopic data. The anti-melanogenic activity of polycarpol was evaluated in α-MSH-stimulated B16F10 murine melanoma cells, a commonly used cellular model of melanogenesis. Polycarpol reduced α-melanocyte-stimulating hormone-induced cellular tyrosinase activity and melanin production at concentrations that did not markedly affect cell viability. Notably, 2 μg/mL (4.54 μM) polycarpol showed a melanin-inhibitory effect comparable to that of arbutin. Western blot analysis showed that polycarpol decreased the expression of microphthalmia-associated transcription factor, tyrosinase, and tyrosinase-related protein-1. In addition, polycarpol suppressed CREB phosphorylation and modulated the MAPK signaling pathways. These findings suggest that polycarpol inhibits melanogenesis through regulation of MITF-associated melanogenic signaling. Overall, this study demonstrates that cultured G. lucidum mycelia can produce anti-melanogenic triterpenoids and highlights cultured mycelial biomass as a controllable fungal material for exploring anti-melanogenic triterpenoids, although further optimization is required to improve production efficiency. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)

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31 pages, 13775 KB

Open AccessArticle

Establishment of CRISPR/Cas9 Genome Editing in Ganoderma boninense and Functional Validation of Hydrophobin-2 as a Virulence Determinant

by Anis Farhan Fatimi Ab Wahab, Mohd Azinuddin Ahmad Mokhtar, Sharmilah Vetaryan and Yang Ping Lee

J. Fungi 2026, 12(8), 594; https://doi.org/10.3390/jof12080594 - 11 Aug 2026

Viewed by 511

Abstract

Oil palm is a major commodity crop in Southeast Asia, particularly in Malaysia and Indonesia, but its productivity is severely threatened by basal stem rot (BSR) and upper stem rot (USR) caused by the white-rot fungus Ganoderma boninense. Infected palms can lose up to 80% yield and die within 6–24 months (young) or 2–3 years (mature). Despite extensive field management efforts, disease incidence continues to rise, especially after replanting. Understanding infection mechanisms and validating fungal virulence factors are crucial for effective control, yet functional genomics in G. boninense has been limited. Previous RNAi-based gene silencing provided initial insights but was constrained by off-target effects and transient activity. Here, we report the first successful application of CRISPR/Cas9 genome editing in G. boninense for functional gene studies. Two genes were targeted: pyrG, essential in uridine monophosphate (UMP) biosynthesis; and hyd-2, encoding a hydrophobin, a potential virulence determinant implicated in host invasion. The disruption of pyrG produced a uracil auxotroph, and the knockout was validated by screening on 5-FOA and validated our system as a functional molecular tool. Disruption of hyd-2 reduced infection capability of the fungus by ~72% to ~91% in vitro. Mutations in both gene disruptions, including insertions, deletions, and substitutions, were confirmed by sequencing. Sequencing analysis also revealed incomplete editing events, as wild-type gene sequences were detected alongside edited alleles in the mutants. Future enhancements should focus on improving editing efficiency of the system. This work establishes a robust platform for functional genetic analysis and dissecting pathogenicity in G. boninense, ultimately advancing strategies to mitigate basal stem rot disease in oil palm. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)

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25 pages, 28849 KB

Open AccessArticle

Mating-Type System Analysis and Domestication of Paramarasmius mesosporus Based on Whole-Genome Sequencing

by Peng Zhu, Junling Wang, Jinjie Du, Shuainan Yang, Boran Zhang, Shuang Gao, Xiao Li, Ao Ma, Zengchi Wang, Jinghua Tian, Ming Li, Guojie Li and Shoumian Li

J. Fungi 2026, 12(8), 579; https://doi.org/10.3390/jof12080579 - 5 Aug 2026

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Abstract

Paramarasmius mesosporus is a wild edible mushroom with a strong aroma and high culinary value, capable of growing at temperatures up to 36 °C. However, its domestication system and the genetic basis of its sexual reproduction remain largely unexplored. In this study, fresh fruiting bodies of P. mesosporus were collected from the rhizosphere of Imperata spp. in saline–alkali land in Hebei Province, China. The species was successfully domesticated for the first time, and fruiting bodies were harvested 7–10 days after spawning. A chromosome-level genome of the monokaryotic strain ‘Q2’ was assembled using whole-genome sequencing, transcriptome analysis, and Hi-C technology, with a total size of 46.57 Mb that was anchored onto 11 pseudochromosomes at a mounting rate of 95.18%. The mating-type system was identified as a typical tetrapolar heterothallic type, with the MAT A and MAT B loci located on chromosomes 2 and 10, respectively. The MAT A locus encodes HD1, HD2, MIP, and β-fg, among which tr-HD1 was found to be pseudogenized due to domain truncation. The MAT B locus comprises seven pheromone receptor genes and seven pheromone precursor genes arranged in an interspersed pattern. Based on these genomic features, a preliminary MAPK signaling pathway model was proposed to elucidate the molecular regulation of sexual reproduction. This study achieved the first artificial domestication and cultivation of P. mesosporus. systematically elucidated genomic characteristics and mating-type molecular mechanisms of this species were systematically elucidated, providing a theoretical foundation for hybrid breeding, molecular marker-assisted selection, and genetic improvement. These findings hold significant scientific and applied value for germplasm innovation and industrial development of this rare edible mushroom. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)

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20 pages, 4144 KB

Open AccessArticle

Identification of Candidate Genes Associated with the Pileus-Deficient Phenotype in Lentinula edodes Through Comparative Genomic and Transcriptomic Analyses

by Bo-Min Seo, Che-Hwon Park, Sung-Chul Lee, Rae-Won Kang and Young-Jin Park

J. Fungi 2026, 12(5), 328; https://doi.org/10.3390/jof12050328 - 1 May 2026

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Abstract

This study aimed to elucidate the molecular mechanisms underlying phenotypic divergence between two Lentinula edodes strains, Le_L and Le_S, which exhibit distinct fruiting body morphologies. While phenotypic variation among mushroom strains has been widely observed, the relative contributions of transcriptional regulation and structural genomic variation to these differences remain poorly understood. Comparative transcriptome analysis identified 8541 differentially expressed genes (DEGs), revealing clear functional divergence between the two strains. Genes upregulated in Le_S were predominantly enriched in ribosomal components and translation-related processes, indicating enhanced protein synthesis activity. In contrast, Le_L-upregulated genes were associated with transporters, transcription factors, and diverse metabolic pathways, suggesting broader regulatory and physiological functions. Protein–protein interaction network analysis further highlighted distinct regulatory architectures, with ribosomal proteins forming highly interconnected hub gene modules in Le_S, whereas Le_L hub genes were functionally diverse and included multiple members of the Major Facilitator Superfamily (MFS). Ortholog analysis across 33 L. edodes strains demonstrated that most hub genes were conserved, indicating their roles as core genetic components. Despite widespread genome-wide variation, including 7931 SNPs and 1149 INDELs, sequence variation within hub genes was limited, and allele-specific expression analysis revealed no significant allelic imbalance. In contrast, presence–absence variation (PAV) analysis identified structural differences affecting MFS transporter genes, which were absent in Le_S but present and upregulated in Le_L. Collectively, these findings suggest that structural genomic variation, particularly involving transporter genes, may play a more prominent role than sequence-level variation in driving phenotypic divergence. This study provides new insights into the genetic basis of strain-specific traits in L. edodes and highlights the importance of integrating multi-level genomic analyses. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)

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23 pages, 4116 KB

Open AccessArticle

Impact of DNA Extraction Strategies on Genomic and Bioinformatic Outcomes in Eight Selected Fungal Strains

by Cyrine Abid, Hela Zouari-Mechichi, Riadh Benmarzoug, Tahar Mechichi and Najla Kharrat

J. Fungi 2026, 12(5), 299; https://doi.org/10.3390/jof12050299 - 22 Apr 2026

Cited by 1 | Viewed by 3163

Abstract

High-quality genomic DNA extraction remains a major bottleneck for fungal genomics, particularly for worldwide aerobic and non-photosynthetic mushroom species that rely on their rigid cell walls, interference between metabolites, polysaccharides, etc., and complex genomes. This study systematically compares five DNA extraction protocols involving four distinct sample preparation procedures (fresh (A), filtered (B), frozen (C) and cryogenic mycelium (D)) across mycelial cultures of eight Tunisian fungal strains representing Ascomycota and Basidiomycota to identify the optimal combination for genomic DNA extraction from mycelium. The eight phylogenetically diverse fungal species were analyzed using short-read (MiSeq and NextSeq550) and/or long-read (MinION Mk1C) sequencing technologies, giving a depth coverage between 3.7× and 83×. The generation and quality of the assemblies were assessed within the Galaxy platform, which revealed a gap percentage of 0–0.509%. Taxonomic characterization and phylogenetic inference were performed with SANGER technology using the Internal Transcribed Spacer (ITS) and D1/D2 region of the 26S rRNA gene, assigning the species to our eight different strains: Clitopilus baronii (BS6), Porostereum spadiceum (BS200), Trametes versicolor (BS22-9), Schizophyllum commune (BS23-13), Gloeophyllum abietinum (BS23-14), Irpex laceratus (BS100), Trichoderma asperellum (GC9) and Trichoderma harzianum (S3). The optimized DNeasy Plant Pro Kit protocol with cryogenic biomass treatment presents a safe and cost-effective method for fungal genome sequencing and taxonomic resolution. This integrated comparative evaluation of extraction for sequencing identifies an optimal Qiagen-based extraction strategy combined with cryogenic treatment for eight diverse Tunisian fungal species, guiding method selection based on specific cell wall characteristics rather than proposing a universal protocol limited by unequal replication and strain numbers. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)

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14 pages, 7394 KB

Open AccessArticle

Unlocking the Potential for Genetic Engineering of the Straw-Degrading Mushroom Stropharia rugosoannulata by Constructing a CRISPR/Cas9 Gene Editing System

by Haibo Hao, Shuzhen Song, Qian Wang, Zongjun Tong, Wen Xu, Jinxiao Yang, Yihong Yue, Tingting Xiao, Yuchen Zhang, Jinjing Zhang and Hui Chen

J. Fungi 2026, 12(4), 269; https://doi.org/10.3390/jof12040269 - 8 Apr 2026

Viewed by 1057

Abstract

The artificially cultivated edible mushroom Stropharia rugosoannulata is widely promoted and cultivated in China because of its ability to efficiently decompose agricultural and forestry waste. However, methods for CRISPR/Cas9 genome editing have not yet been established for S. rugosoannulata. In this study, we identified three SrU6 promoters in S. rugosoannulata and constructed the CRISPR/Cas9 expression vector GPiE-SrU6. Moreover, we found that mutant strains were obtained only when the expression of the single guide RNA (sgRNA) was driven by the SrU6-3 promoter. We subsequently employed a tandemly repeated SrU6-tRNA-sgRNA module to knock out two sites within the ura3 gene. The expression vector was introduced into the mycelium via Agrobacterium-mediated transformation (ATMT). Following dual selection with 60 μg/mL hygromycin (Hyg) and 0.2 mg/mL 5-fluoroorotic acid (5-FOA), stable transformants were obtained and subcultured. The mutation efficiency at the targeted ura3 locus was subsequently assessed. The CRISPR/Cas9 system successfully disrupted the target marker gene (ura3), achieving an editing efficiency of 14.9%. In summary, this study reports the first successful establishment of a CRISPR/Cas9 genome editing system in S. rugosoannulata. This study not only meets a future need for genetic manipulation tools for S. rugosoannulata but also provides a robust platform for engineering superior strains for eco-circular agriculture. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)

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20 pages, 2842 KB

Open AccessArticle

Comparative Mitogenomics Reveals Intron Dynamics and Mitochondrial Gene Expression Shifts in Domesticated and Wild Pleurotus ostreatus

by Gumer Pérez, Idoia Jiménez, Edurne Garde, Lucía Ramírez and Antonio G. Pisabarro

J. Fungi 2026, 12(1), 75; https://doi.org/10.3390/jof12010075 - 20 Jan 2026

Cited by 2 | Viewed by 1514

Abstract

Mitochondrial genomes play a central role in fungal physiology and adaptation, yet their evolutionary dynamics during domestication remain poorly understood. Here, we performed a comparative mitogenomic and gene-expression analysis of three Pleurotus ostreatus dikaryotic strains differing in origin and degree of adaptation to laboratory conditions: the long-term commercial strain dkN001, the laboratory-maintained wild isolate dkF515, and the recently collected wild strain dkN009. High-throughput Illumina sequencing enabled complete assembly of circular mitochondrial genomes, revealing substantial size variation among strains, where the dkN001 strain exhibited the second smallest mitogenome reported for the genus Pleurotus. Comparative analyses showed >99% sequence identity between wild isolates and ~95% identity relative to the commercial strain. Variations in genome size among strains were associated with intron dynamics in the cox1 and rnl genes, as well as intron loss predominantly in the commercial strain dkN001, consistent with mitochondrial genome streamlining during domestication. Expression profiling of mitochondrial protein-coding genes (PCGs) under multiple culture conditions revealed conserved transcriptional responses in dkN001 and dkF515 that contrasted sharply with those of dkN009. The differences observed, which affected components of the electron transport chain, suggested shifts in energy metabolism associated with long-term laboratory maintenance. Therefore, our results demonstrate that domestication in P. ostreatus involves both structural remodelling of the mitogenome and changes in regulation of mitochondrial PCGs, highlighting the importance of mitonuclear interactions in fungal adaptation to controlled environments. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)

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Review

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23 pages, 3767 KB

Open AccessReview

Molecular Advances and Sustainable Strategies in Mushroom Production for Food Security: A Review

by Dali V. Francis, Malu Kishorkumar, Zienab F. R. Ahmed, Elke G. Neumann and Shyam S. Kurup

J. Fungi 2026, 12(3), 205; https://doi.org/10.3390/jof12030205 - 11 Mar 2026

Cited by 1 | Viewed by 2161

Abstract

Mushrooms offer a promising solution for sustainable food production due to their nutritional value, low resource requirements, and ability to grow in diverse environments. As interest in mushrooms grows, it is important to understand where current research is focused and where key gaps remain. A bibliometric analysis of 776 research articles indexed in Web of Science revealed a strong emphasis on yield, substrate reuse, and enzymatic degradation, but limited attention to molecular approaches, climate adaptation, and studies from arid regions such as the Middle East. Building on these findings, this review explores the ecological diversity of mushrooms and their adaptations across tropical, temperate, boreal, and arid ecosystems. It discusses the role of mycorrhizal and microbial interactions in nutrient cycling and environmental resilience, including desert truffle symbioses. Key pathways and genetic regulation involved in lignin degradation are outlined, along with recent advancements in transcriptomics, proteomics, genomics, metabolomics, and metagenomics that support improved cultivation and bioactive compound production. The review also addresses sustainable practices, such as microbiome integration and resource recycling, to enhance mushroom farming. The aim is to bring together ecological insights and molecular strategies to support sustainable mushroom production, particularly in regions facing resource and climate challenges. Full article

(This article belongs to the Special Issue Molecular Biology of Mushroom, 2nd Edition)

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