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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: 31 March 2026 | Viewed by 5703

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Prof. Dr. Chengwei Liu

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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
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Dr. Jianzhao Qi

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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
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Dr. Xiuzhang Li

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Guest Editor

State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China
Interests: plant protection; edible and medicinal fungi resources
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-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

metabolomics
genomics
multi-omics
metabolic pathway
biosynthesis

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Related Special Issue

Fungal Metabolomics and Genomics in Journal of Fungi (19 articles)

Published Papers (9 papers)

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Research

16 pages, 6172 KB

Open AccessArticle

Identification and Transcriptomic Analyses of Two Endophytic Fungi WDR2 and WDR5 from Wild Soybean Elucidates Mechanistic Aspects of Alkali Stress Tolerance

by Jiali Tian, Xuan Liu, Shixi Lu, Xuan Dong, Yujie Chen, Siqi Hou, Tianyu Lei, Xinyu Li, Ruixin Cao, Yue Su, Xiaodong Ding, Qiang Li and Jialei Xiao

J. Fungi 2026, 12(2), 114; https://doi.org/10.3390/jof12020114 - 5 Feb 2026

Abstract

Soil alkalinization constitutes a significant abiotic stress factor that severely constrains global agricultural productivity. The application of alkali-tolerant endophytes represents a promising strategy for enhancing crop resilience. This study focused on the isolation and characterization of alkali-resistant endophytic fungi derived from wild soybean (Glycine soja), aiming to elucidate their potential in promoting host plant growth and to investigate their molecular responses to alkali stress. From an initial collection of 39 wild soybean endophytic fungal isolates, 12 strains demonstrated significant alkali tolerance, as evidenced by increased mycelial dry weight under both mild and intense alkali stress. Among these, two strains, designated WDR2 and WDR5, demonstrated particularly pronounced biomass enhancement and were taxonomically identified as Fusarium verticillioides through comprehensive morphological and molecular analyses. Subsequent inoculation assays conducted on maize (Zea mays) revealed that both fungal strains significantly alleviated the inhibitory effects of alkali stress on root system architecture. Comparative evaluations in soybean indicated that the growth-promoting effects of these endophytes were host-specific and varied according to fungal strain, stress intensity, and inoculation timing. Transcriptomic profiling via RNA-Seq under mild alkali stress identified 589 and 182 differentially expressed genes (DEGs) in WDR2 and WDR5, respectively, with only 43 DEGs shared between the two strains, indicating largely strain-specific transcriptional adaptations. Functional enrichment analysis revealed several shared mechanisms underlying alkaline adaptation in both fungi species, including the maintenance of ion homeostasis, remodeling of the cell wall, and regulation of protein complex assembly and oxidative stress responses. Moreover, distinct metabolic adaptations were identified: WDR2 exhibited significant enrichment in cellular integrity and modulation of membrane-related processes, as well as amino sugar and nucleotide sugar metabolism pathways. In contrast, WDR5 was enriched in phosphate ion transport and related transporter functions, glycerol kinase activity, and glycerolipid and glutathione metabolism. In summary, this study successfully identified two novel alkali-tolerant wild soybean endophytic fungi, WDR2 and WDR5. The results provide valuable insights into their divergent molecular adaptation strategies and highlight their potential application as bio-inoculants to enhance crop productivity in alkaline soils. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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24 pages, 6844 KB

Open AccessArticle

Arbuscular Mycorrhizal Fungi-Mediated Reconfiguration of Poplar Leaf C-N-P Metabolic Networks: Environment-Dependent Synergies and Nutrient Interactions

by Xiaan Tang, Mengmeng Chen, Panpan Meng and Junyu Song

J. Fungi 2026, 12(2), 105; https://doi.org/10.3390/jof12020105 - 2 Feb 2026

Viewed by 89

Abstract

The regulatory mechanisms by which AMF modulate the integrated carbon (C)-nitrogen (N)-phosphorus (P) metabolic network in woody plant leaves remain unclear. We investigated how varying nitrate (NO₃⁻) and phosphate (Pi) supply, with or without AMF inoculation, reshapes the leaf metabolic network in poplar seedlings. Key findings reveal that AMF acts as a central metabolic hub, optimizing C-N-P coordination in an environment-dependent manner. Under low Pi, NO₃⁻ supply enhanced P remobilization and photosynthetic efficiency, boosting growth. AMF further optimized low-Pi adaptation by promoting P storage and buffering, significantly improving photosynthesis and biomass. Under high Pi, NO₃⁻ supply shifted focus towards enhancing Rubisco-mediated carbon assimilation. AMF synergistically improved carbon assimilation efficiency and suppressed non-essential P recycling. N metabolism effects of Pi were contingent on NO₃⁻ availability, and AMF reprogrammed N assimilation pathways accordingly, balancing uptake and utilization under different N regimes. Critically, AMF orchestrated environment-specific metabolic adjustments, reinforcing P buffering and photosynthetic gain under Pi limitation, and enhancing C assimilation efficiency while minimizing P waste under Pi sufficiency. This study demonstrates that poplar leaf C-N-P networks are reconfigured through N-P synergisms modulated by AMF, positioning AMF as a pivotal integrator of nutrient acquisition and allocation. These insights provide a physiological foundation for developing efficient forestry nutrient management and mycorrhizal application strategies. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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23 pages, 14339 KB

Open AccessArticle

Integrative Genomic and Transcriptomic Analysis of White-Rot Fungi Ganoderma tsugae Growing on Both Coniferous and Broad-Leaved Trees

by Yifei Sun, Mengxue Lv, Meiqin Luo, Ziqi Yao, Miao Zhou, Yuxuan Fang, Dongmei Wu, Neng Gao and Baokai Cui

J. Fungi 2026, 12(1), 35; https://doi.org/10.3390/jof12010035 - 1 Jan 2026

Viewed by 531

Abstract

Ganoderma tsugae is a typical white-rot fungus capable of decaying both coniferous and broad-leaved trees and is also used in traditional Chinese medicine for its immunomodulatory and anticancer properties. To elucidate the molecular basis of its broad substrate adaptability, we performed integrated genomic and transcriptomic analyses of two G. tsugae strains (collected from Xingjiang on Betula and Jilin on Larix). The high-quality genomes of G. tsugae Wu 2022 from Xinjiang (40.8 Mb, 12,496 genes) and G. tsugae Cui 14110 from Jilin (45.6 Mb, 13,450 genes) were obtained. There are enriched gene families related to carbohydrate-active enzymes (CAZymes) in two G. tsugae strains. Notably, specific CAZyme families implicated in hemicellulose (GH16), chitin metabolism (GH18), and ester bond cleavage (CE10) were prominently expanded. Transcriptome analyses under the induction of Betula and Larix sawdust revealed a core adaptive response. A total of 5558 genes were differentially expressed, including 2094 up-regulated and 3464 down-regulated genes. Most differentially expressed genes (DEGs) were annotated as “catalytic activity”, “metabolic processes” and specific functions such as nutrient transport (“MFS transporter”), and lipid metabolism (“3-oxoacyl-[acyl-carrier protein] reductase”). In addition, a conserved suite of the eleven shared DEGs were annotated as “Heat shock protein 9/12”, “alcohol dehydrogenase”, and “Cytochrome p450” related to secondary metabolites biosynthesis, transport, and catabolism. Based on the annotation results, the wood degradation mechanism of G. tsugae can be described as synthesizing and secreting degradation enzyme system to obtain energy, using protective enzyme systems to ensure its own health, and employing a transport enzyme system to recycle metabolic capacity. This progress ensures the environmental adaptability and high degradation efficiency of G. tsugae during wood degradation. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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13 pages, 891 KB

Open AccessArticle

Genome Mining and Heterologous Reconstitution of a PKS-NRPS Gene Cluster from Aspergillus flavipes LY1-5 Affords Structurally Novel Tetronates

by Quan Dai, Yiqiao Li, Shuzhe Lv, Shuang Zhao, Liyuan Han, Jiaxin Xu, Hui Shuai, Youming Zhang and Fu Yan

J. Fungi 2026, 12(1), 28; https://doi.org/10.3390/jof12010028 - 29 Dec 2025

Viewed by 497

Abstract

Heterologous expression of silent biosynthetic gene clusters represents a key strategy for the discovery of structurally novel natural products. In this study, we obtained ten new tetronate natural products, designated as talactones A–J (1–10), through heterologous expression of a polyketide synthase–nonribosomal peptide synthetase (PKS-NRPS) gene cluster (tho) from the fungus Aspergillus flavipes LY1-5 in A. nidulans A1145. Their structures were elucidated by comprehensive HR-ESI-MS and NMR analyses. Notably, talactone A (1) contains a rare 1,4-thiazepane scaffold, whereas talactones B (2) and C (3) feature a novel 2,3-dihydrofuro [3,4-b]pyridine-4,5(1H,7H)-dione skeleton. Biosynthetic investigations indicate that the 1,4-thiazepane ring in 1 arises from a non-enzymatic reaction between a tetronate acid and cysteine, while 2 and 3 are derived from 5 and 6, respectively, via spontaneous intramolecular cyclization under acidic conditions. Antibacterial activity assays revealed that compounds 1–3, 9, and 10 exhibit moderate antibacterial effects. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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15 pages, 1712 KB

Open AccessArticle

Screening of Monokaryotic Strains of Ganoderma sichuanense for Gene Editing Using CRISPR/Cas9

by Le Li, Yuxuan Liu, Jianzhong Wu, Nuan Wen, Yang Song, Xue Wang, Zhuang Li, Huiying Sun and Yongping Fu

J. Fungi 2026, 12(1), 25; https://doi.org/10.3390/jof12010025 - 28 Dec 2025

Cited by 1 | Viewed by 466

Abstract

Ganoderma sichuanense is a widely used medicinal and edible fungus. Genomic studies have revealed substantial genetic variation among its different strains, indicating that a genetic transformation system optimized for one genotype may not be effective in others. However, no study has systematically evaluated the efficiency of a genetic transformation system across diverse genotypes, which has potentially limited functional genetic studies in this species. In this study, we first evaluated eight wild and cultivated monokaryotic strains with different genotypes based on their hygromycin B resistance and green fluorescent protein (GFP) expression efficiency. Three strains (CCMJ1500101, CCMJ1509001, and CCMJ1507802) were identified as capable of stable foreign gene expression, achieving transformation efficiencies of 20.0–66.7% via PEG-mediated protoplast transformation. Subsequently, a CRISPR/Cas9 system incorporating seven key elements to enhance editing efficiency was constructed and applied to these three strains using the ura3 gene as a test target. Gene editing efficiencies varied significantly among genotypes, ranging from 14.3% to 75.0%, confirming the system’s high efficacy and genotype dependence. Importantly, to rigorously assess the robustness and versatility of the established transformation platform, we further validated its broad applicability in the best-performing strain, CCMJ1500101, by successfully editing five functional genes involved in growth, development, and metabolism. Notably, gene inversion events were detected for the first time in edited transformants of Ganoderma, providing new clues for understanding non-homologous end joining (NHEJ) repair in this species. This study establishes a robust dual-sgRNA CRISPR/Cas9 platform for G. sichuanense and provides valuable strain resources to facilitate future gene functional studies and genetic improvement. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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18 pages, 2984 KB

Open AccessArticle

Integrated Transcriptomic and Metabolomic Profiling Reveals Monotonic Molecular Signatures During Fruiting Body Development of Coprinus comatus

by Zhu Liu, Linzhi Kang, Yangyang Peng, Jianhao Wang, Luyao Ye, Hui Zhou and Ming Liu

J. Fungi 2025, 11(12), 849; https://doi.org/10.3390/jof11120849 - 29 Nov 2025

Viewed by 618

Abstract

Integrative transcriptomic–metabolomic profiling across three developmental stages of Coprinus comatus revealed that a coherent, monotonic molecular program drives fruiting body maturation. Stage-resolved RNA-seq and untargeted metabolomics were carried out to cleanly separate samples, and results showed directional trends: glycerophospholipids and other lipid species declined steadily, whereas peptides and amino-acid derivatives accumulated. Early development was driven by cell cycle regulation and DNA damage repair, while later stages shifted toward amino acid, glutathione and cell wall metabolism. These coupled transcriptional and metabolic shifts delineate processes associated with maturation and autolysis from which actionable markers can be identified to refine cultivation practices and optimize harvesting time. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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21 pages, 6757 KB

Open AccessArticle

Untargeted Metabolomics-Based Characterization of the Metabolic Profile and Antioxidant Activity of Ophiocordyceps sinensis and Its Substitutes

by Bing Jia, Haoxu Tang, Chuyu Tang, Chao Feng, Yuling Li and Xiuzhang Li

J. Fungi 2025, 11(10), 740; https://doi.org/10.3390/jof11100740 - 16 Oct 2025

Viewed by 979

Abstract

Ophiocordyceps sinensis represents a valuable medicinal resource. In this study, mechanisms underlying differences in chemical composition and antioxidant capacity among wild O. sinensis (GL), artificially cultivated O. sinensis (RG), and product of O. sinensis “Bailing” capsules (BL) were systematically investigated via in vitro antioxidant capacity assays and untargeted metabolomics. Results showed GL exhibited the highest total phenol (TPS) content and superior free radical scavenging activity. Additionally, superoxide dismutase (SOD) and peroxidase (POD) activities in RG were higher than those in BL. Correlation analysis of antioxidant indices demonstrated significant positive correlations between total phenols (TPS) and flavonoids (TF) with DPPH radical scavenging, ferric ion reducing antioxidant power (FRAP), hydroxyl radical scavenging rate, and superoxide anion radical scavenging rate (p < 0.01). A total of 6729 metabolites were detected, encompassing amino acids and their derivatives, lipids, and nucleotides and their derivatives, among other classes. Furthermore, metabolites exhibited distinct intergroup separation, indicating significant differences in metabolic profiles between O. sinensis and its substitute products. KEGG enrichment analysis showed that differential metabolites were mainly enriched in amino acid, lipid, and nucleotide metabolic pathways, among which the linoleic acid metabolic pathway was significantly downregulated. Key metabolites included γ-linolenic acid, 12(13)-EpOME-d, 9-HpODE, etc. Additionally, results of correlation analysis revealed that differential metabolites of lipids, nucleotides, and amino acids exhibited a significant positive correlation with antioxidant indices (p < 0.05). These findings suggest that the antioxidant capacity of O. sinensis and its substitutes may be regulated via linoleic acid metabolism, providing a theoretical basis for advancing targeted functional development of O. sinensis and its substitute products. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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22 pages, 4646 KB

Open AccessArticle

Analysis of Amino Acid and Derivative Diversity and Antioxidant Capacity in Ophiocordyceps sinensis and Its Substitutes

by Haoxu Tang, Bing Jia, Chuyu Tang, Chao Feng, Yuling Li and Xiuzhang Li

J. Fungi 2025, 11(10), 711; https://doi.org/10.3390/jof11100711 - 30 Sep 2025

Viewed by 1004

Abstract

In this study, we used liquid chromatography–tandem mass spectrometry (LC-MS/MS) combined with multivariate statistical analysis to conduct comprehensive qualitative and quantitative profiling of amino acids and their derivatives in wild Ophiocordyceps sinensis (O. sinensis) samples from Naqu (NQ) and Xiaojin (XJ), cultivated O. sinensis (RG), and Bailing Capsules (BL). The objective was to systematically characterize amino acid metabolism and assess its correlation with antioxidant functionality. A total of 82 amino acids and their derivatives were identified. XJ had the highest essential amino acids, while BL had significantly lower content (except lysine) (p < 0.05). Antioxidant assays revealed that NQ and XJ samples exhibited superior antioxidant activity in 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonate) (ABTS), 2,2-diphenyl-1-picrylhydrazyl (DPPH), and ferric ion reducing antioxidant power (FRAP) assays, and this activity showed a correlation to the contents of bioactive components such as total phenols (TPS), total polysaccharide (TPE), and total flavonoids (TF). Further pathway analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) suggested that arginine and proline metabolism, aromatic amino acid biosynthesis, and tryptophan metabolism may be critical pathways that could underpin regional differences in O. sinensis quality, while variation in tyrosine metabolism may account for differences in antioxidant activity. This study provides a systematic comparison of amino acid profiles and antioxidant capacities across O. sinensis and its substitutes, offering a robust theoretical foundation for the development and functional evaluation of these bioresources. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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19 pages, 7841 KB

Open AccessArticle

Co-Expression Network Analysis Suggests PacC Transcriptional Factor Involved in Botryosphaeria dothidea Pathogenicity in Chinese Hickory

by Dong Liang, Yiru Jiang, Wei Ai, Yu Zhang, Chengxing Mao, Tianlin Ma and Chuanqing Zhang

J. Fungi 2025, 11(8), 580; https://doi.org/10.3390/jof11080580 - 4 Aug 2025

Viewed by 1063

Abstract

Botryosphaeria dothidea is the causative agent of Chinese hickory trunk canker, which poses significant threat to the production of Chinese hickory (Carya cathayensis Sarg.). Previous studies reported that endophytic–pathogenic phase transition, also referred to as latent infection, plays an important role in the interaction of Botryosphaeria dothidea with various host plants, including Chinese hickory. However, the mechanism underlying this phase transition is not well understood. Here, we employed RNA-Seq to investigate transcriptional changes in B. dothidea during its phase transition upon interaction with Chinese hickory. A co-expression network was generated based on 6391 differentially expressed genes (DEGs) identified from different infection stages and temperature treatments. One co-expressed module was found that highly correlated with temperature treatments which simulated conditions of B. dothidea latent infection in the field. Subsequently, 53 hub genes were detected, and gene ontology (GO) enrichment analysis revealed three categories of enriched GO terms: transmembrane transport or activity, ion homeostasis or transport, and carbohydrate metabolism. One PacC transcriptional factor (BDLA_00001555, an ambient pH regulator), and one endo-β-1,3-glucanase (BDLA_00010249) were specifically upregulated under temperature treatments that corresponded with the activation stage of B. dothidea’s pathogenic state. The knockout mutant strain of BDLA_00001555 demonstrated defective capability upon the activation of the pathogenic state. This confirmed that BDLA_00001555, the PacC transcriptional factor, plays an important role in the latent infection phase of B. dothidea. Our findings provide insights into the pathogenic mechanism of Chinese hickory trunk canker disease. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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