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Molecular Biology of Mushroom, 2nd Edition
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Molecular Biology of Mushroom, 2nd Edition

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: 30 September 2026 | Viewed by 3229

Special Issue Editor

Dr. Young-Jin Park

E-Mail Website
Guest Editor
Department of Medicinal Biosciences, Konkuk University, Chungju 27478, Republic of Korea
Interests: genomics; transcriptomics; medicinal mushroom metabolite; epigenetics; cultivation; system biology
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 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

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

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Related Special Issue

Published Papers (5 papers)

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Research

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20 pages, 4144 KB  
Article
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
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 [...] Read more.
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  
Article
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
Viewed by 547
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 [...] Read more.
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  
Article
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 398
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, [...] Read more.
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  
Article
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
Viewed by 820
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 [...] Read more.
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  
Review
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
Viewed by 916
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 [...] Read more.
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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