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Fungal Metabolomics and Genomics, 3rd Edition
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Fungal Metabolomics and Genomics, 3rd Edition

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

Deadline for manuscript submissions: 31 January 2027 | Viewed by 3090

Editors

Prof. Dr. Chengwei Liu

E-Mail Website
Guest Editor
Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
Interests: fungal synthetic biology; natural product chemistry; biosynthetic pathway
Special Issues, Collections and Topics in MDPI journals
Dr. Jianzhao Qi

E-Mail Website
Guest Editor
Edible Fungi Center, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
Interests: exploration and genetic evolution of macrofungi germplasm resources; structural identification and activity evaluation of fungus natural active ingredients derived; biosynthesis and green manufacturing of active ingredients
Special Issues, Collections and Topics in MDPI journals
Dr. Xiuzhang Li

E-Mail Website
Guest Editor
State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China
Interests: plant stress biology; edible and medicinal fungi; grass endophyte; multi-omics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metabolomics and genomics have had major impacts on fungal research. This Special Issue of the JoF is dedicated to exploring the frontiers of these aspects, highlighting the latest breakthroughs and innovative approaches in these dynamic fields. We aim to present a collection of research that delves into the molecular mechanisms of fungi, providing insights into their genetic makeup, metabolic pathways, and the regulation of these processes.

We encourage contributions from metabolomics- and genomics-related studies, and we welcome studies on transcriptomics and proteomics, as well as multi-omics interactions. Original research, reviews, and communications are all welcome. We are excited to showcase the innovative work of our contributors and hope this Special Issue will bring insights to the scientific community.

Prof. Dr. Chengwei Liu
Dr. Jianzhao Qi
Dr. Xiuzhang Li
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-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

  • metabolomics
  • genomics
  • multi-omics
  • metabolic pathway
  • biosynthesis

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Published Papers (6 papers)

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Research

20 pages, 7584 KB  
Article
Breeding of Early Maturity, High-Quality Auricularia heimuer Strains Using Protoplast Fusion
by Xin Yue, Shuyuan Song, Xiaojia Zhang, Yanshu Zhao, Yuxin Jiang, Shuyang Zhou, Xiancheng Zhang, Chuang Han and Xiaodong Dai
J. Fungi 2026, 12(8), 591; https://doi.org/10.3390/jof12080591 - 10 Aug 2026
Viewed by 281
Abstract
Auricularia heimuer is an important cultivated edible mushroom in China. This study used the early maturity, chrysanthemum-shaped, high yield strain “8808” and the late-maturity, single-shaped, high-quality strain “HW15” as parental strains. The objective was to develop a new strain of A. heimuer combining [...] Read more.
Auricularia heimuer is an important cultivated edible mushroom in China. This study used the early maturity, chrysanthemum-shaped, high yield strain “8808” and the late-maturity, single-shaped, high-quality strain “HW15” as parental strains. The objective was to develop a new strain of A. heimuer combining early maturity with excellent quality through protoplast fusion. Protoplasts from the parental strains were fused using a polyethylene glycol (PEG)-mediated method. The obtained hybrids were identified through clamp connection, antagonism tests, esterase isozyme analysis, and Inter-Simple Sequence Repeat (ISSR) molecular marker techniques, followed by ultimate selection through cultivation. Among the evaluated hybrids, strain R33 exhibited desirable agronomic traits: primordium formation occurred 4 days earlier than the parental strain HW15, harvest time was advanced by 6 days, yield increased by 14.7%, and the ratio of absorbed water improved by 29.8%. Transcriptomic analysis revealed that starch and sucrose metabolism as well as amino acid metabolism pathways were significantly upregulated in R33, which may be associated with its early maturity and high-yield phenotype. Overall, protoplast fusion technology can be used to create promising candidate strains that combine early maturity, high yield, and excellent quality. Full article
(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 3rd Edition)
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13 pages, 7176 KB  
Article
Transcriptomics and Physiological Analysis Reveal Response Strategies of Sanghuangporus baumii to Aluminum Exposure
by Xinyu Tong, Anxin Wang, Zengcai Liu and Li Zou
J. Fungi 2026, 12(8), 586; https://doi.org/10.3390/jof12080586 - 7 Aug 2026
Viewed by 304
Abstract
Sanghuangporus baumii, a medicinal macrofungus, remains unexplored in its response to aluminum stress, despite the widespread environmental relevance of this metal. This study investigated the dose-dependent effects of Al3+ on mycelial growth and metabolic regulation. Exposure to 1 mM Al3+ [...] Read more.
Sanghuangporus baumii, a medicinal macrofungus, remains unexplored in its response to aluminum stress, despite the widespread environmental relevance of this metal. This study investigated the dose-dependent effects of Al3+ on mycelial growth and metabolic regulation. Exposure to 1 mM Al3+ moderately stimulated growth (1.11-fold of control) and induced mild oxidative stress, which activated an effective antioxidant response—including increased SOD, CAT, and POD activities and elevated reduced glutathione content—thereby maintaining redox balance and increasing soluble sugar content. In contrast, 10 mM Al3+ led to pronounced intracellular Al3+ accumulation, severe growth inhibition, and marked oxidative damage, accompanied by impairment of the antioxidant system, yet a marked increase in total triterpenoid content (1.72-fold). Transcriptomic analysis identified 642 and 3019 differentially expressed genes (DEGs) in the 1 and 10 mM Al3+ treatments, respectively. KEGG enrichment analysis revealed concentration-dependent alterations in pathways related to peroxisome function, glutathione metabolism, starch and sucrose metabolism, and terpenoid backbone biosynthesis. Collectively, these findings suggest that Al3+ modulates S. baumii growth and metabolism in a dose-dependent manner, with redox remodeling as a potential mechanism, offering novel insights into fungal metal adaptation and the targeted modulation of medicinal metabolite production. Full article
(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 3rd Edition)
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14 pages, 3412 KB  
Article
Metabolic Reprogramming During Heat Stress and Short-Term Recovery in Oudemansiella raphanipes Revealed by Integrated Metabolomics and Transcriptomics
by Yangyang Peng, Jianhao Wang, Lingjun Xu, Nan Liao, Yan Hai, Zitian Xiao, Jiang Xu and Ming Liu
J. Fungi 2026, 12(8), 557; https://doi.org/10.3390/jof12080557 - 28 Jul 2026
Viewed by 302
Abstract
Temperature constrains stable mycelial growth and production of Oudemansiella raphanipes, but its molecular response to heat stress followed by recovery remains insufficiently resolved. We integrated untargeted LC-MS metabolomics and RNA sequencing to compare control mycelia maintained at 28 °C (HPJZ28) with mycelia [...] Read more.
Temperature constrains stable mycelial growth and production of Oudemansiella raphanipes, but its molecular response to heat stress followed by recovery remains insufficiently resolved. We integrated untargeted LC-MS metabolomics and RNA sequencing to compare control mycelia maintained at 28 °C (HPJZ28) with mycelia exposed to 42 °C for 6 h and then allowed to recover at 28 °C for 2 h (HPJZ42-R). Metabolomic and transcriptomic profiles separated clearly between the two conditions, indicating broad post-heat recovery-associated molecular remodeling. Most differential metabolites were lower in HPJZ42-R, whereas a smaller subset accumulated, suggesting selective metabolic reorganization rather than generalized activation. Transcriptome analysis identified extensive gene-expression remodeling, with 1081 upregulated and 1878 downregulated genes in the HPJZ28 versus HPJZ42-R comparison. Pathway-level analyses implicated central carbon metabolism, lipid metabolism, amino acid metabolism, peroxisome-related processes, and calcium signaling. Because the sampling design included a recovery period and a single post-stress time point, integrated gene–metabolite correlations are interpreted as exploratory associations rather than evidence of direct regulatory coupling. These results provide species-level multi-omics evidence for the post-heat recovery state of O. raphanipes and identify candidate pathways for future functional and physiological validation. Full article
(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 3rd Edition)
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16 pages, 6960 KB  
Article
Transcriptomic Profiling of Developmental Stages and Screening of Candidate Genes in Pholiota nameko
by Yao Zhu, Tingting Ma, Yichu Wang, Jiayi Liu, Xiaolong He, Junshen Wang, Pengfei Jin and Xiaopeng Gao
J. Fungi 2026, 12(7), 542; https://doi.org/10.3390/jof12070542 - 22 Jul 2026
Viewed by 365
Abstract
The developmental cycle of Pholiota nameko can be divided into four stages: the mycelial stage (JS), the primordium stage (FH), the growth stage (SZ), and the maturity stage (CS). In this study, transcriptome sequencing was performed on P. nameko at these four stages, [...] Read more.
The developmental cycle of Pholiota nameko can be divided into four stages: the mycelial stage (JS), the primordium stage (FH), the growth stage (SZ), and the maturity stage (CS). In this study, transcriptome sequencing was performed on P. nameko at these four stages, followed by the screening of differentially expressed genes and functional annotation via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. By integrating the annotation results of all differentially expressed genes (DEGs), we screened for candidate genes potentially correlated with the growth and development of P. nameko. The expression levels of these candidate genes were then compared using real-time quantitative PCR (RT-qPCR) to identify those with the highest expression. The results showed that in the FH vs. CS and SZ vs. CS comparisons, DEGs were mainly enriched in pathways related to protein processing, fatty acid metabolism, and linoleic acid metabolism, suggesting that alterations in these specific metabolic pathways may be closely associated with the growth and development of P. nameko. Through analysis based on upregulation and log2 fold change (log2FC) values, further screening identified 13 candidate genes, and the gene Cluster-7415.13 with the highest expression level was preliminarily screened out through RT-qPCR analysis. This gene may be potentially involved in processes such as rapid cell expansion, cell wall synthesis, nutrient absorption, and active growth-stage metabolism. Full article
(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 3rd Edition)
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23 pages, 4571 KB  
Article
Telomere-to-Telomere Genome Assembly of Coprinellus disseminatus and Genomic Insights into Its Symbiotic Germination of Cremastra appendiculata Seeds
by Wenyan Huo, Xuelian He, Jing Su, Lu Dai, Peng Qi, Yu Liu, Liguang Zhang, Ting Qiao and Junzhi Li
J. Fungi 2026, 12(7), 460; https://doi.org/10.3390/jof12070460 - 23 Jun 2026
Viewed by 559
Abstract
Cremastra appendiculata is a medicinally important orchid whose seed germination depends on fungal symbionts. Here, we present the first telomere-to-telomere (T2T) genome assembly of the orchid mycorrhizal fungus Coprinellus disseminatus, comprising 15 gapless chromosomes (54.41 Mb) with 98.80% BUSCO completeness. Symbiotic germination [...] Read more.
Cremastra appendiculata is a medicinally important orchid whose seed germination depends on fungal symbionts. Here, we present the first telomere-to-telomere (T2T) genome assembly of the orchid mycorrhizal fungus Coprinellus disseminatus, comprising 15 gapless chromosomes (54.41 Mb) with 98.80% BUSCO completeness. Symbiotic germination assays demonstrated that C. disseminatus significantly outperformed its congeners C. domesticus and C. radians in protocorm biomass. Comparative genomic analyses revealed highly conserved carbohydrate-active enzyme (CAZyme) repertoires among the three species, ruling out CAZyme divergence as the primary driver of differential symbiotic performance. CAFE analysis showed that since its divergence approximately 117.8 million years ago, C. disseminatus underwent substantial gene family expansions enriched in proteasome, endocytosis, adherens junction, and tight junction pathways, suggesting that lineage-specific expansion of these functional modules may have contributed to its superior symbiotic capacity for orchid seed germination. These findings require further experimental validation through transcriptomic and functional genomic approaches. Full article
(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 3rd Edition)
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14 pages, 3331 KB  
Article
Effects of Different Initial pH Conditions on the Antioxidant Capacity and Lipidomic Profiles of Samsoniella hepialid
by Yan Tong, Chuyu Tang, Bing Jia, Haoxu Tang, Jinxuan Yan, Yuling Li and Xiuzhang Li
J. Fungi 2026, 12(5), 367; https://doi.org/10.3390/jof12050367 - 16 May 2026
Cited by 1 | Viewed by 716
Abstract
Samsoniella hepiali produces an array of pharmacologically valuable metabolites, but how environmental pH regulates its antioxidant system and lipid metabolism during submerged fermentation remains unclear. This study aimed to investigate the effects of different initial culture pH values (pH 4, 5, 6, and [...] Read more.
Samsoniella hepiali produces an array of pharmacologically valuable metabolites, but how environmental pH regulates its antioxidant system and lipid metabolism during submerged fermentation remains unclear. This study aimed to investigate the effects of different initial culture pH values (pH 4, 5, 6, and 7) on the antioxidant capacity and lipidomic metabolism of S. hepiali. The results demonstrated that at pH 5, the activities of peroxidase (POD) and superoxide dismutase (SOD), the contents of total phenolics (TP) and flavonoids, the scavenging rates of DPPH• and •OH, and the total antioxidant capacity all peaked. Conversely, the level of glutathione (GSH) reached its maximum at pH 6 (0.69 ± 0.014 μmol/g). Lipidomic analysis identified a total of 404 lipid molecular species, mainly TG, PE, and DG. Comparative analysis among pH 4 vs. pH 5, pH 6 vs. pH 5, and pH 7 vs. pH 5 revealed 27 core DALs belonging to 11 lipid subclasses, most of which were upregulated at pH 5. KEGG pathway enrichment analysis further revealed that sphingolipid metabolism was the sole core co-enriched pathway under different pH conditions. Particularly at pH 5, key signaling lipids, such as ceramides, underwent pronounced targeted accumulation. This study elucidates the molecular adaptation mechanisms of medicinal fungi in response to pH variation from a lipidomic perspective. It provides a basis for optimizing fermentation conditions to enhance antioxidant activity and functional lipid production. Full article
(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 3rd Edition)
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