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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 May 2025 | Viewed by 7542

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Special Issue Editors

Prof. Dr. Chengwei Liu

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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

Dr. Jianzhao Qi

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Guest Editor

Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, China
Interests: structure identification and activity evaluation of natural active ingredients from macrofungi (mushrooms); biosynthesis and green manufacturing of active ingredients of medicinal fungi; nuclear and mitochondrial genomes of macrofungi, and their inheritance and evolution

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 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

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Keywords

metabolomics
genomics
multi-omics
metabolic pathway
biosynthesis

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Published Papers (11 papers)

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Research

21 pages, 6272 KiB

Open AccessArticle

Whole-Genome Characterization of Inonotus hispidus from Ulmus macrocarpa and Its Comparative Genomics with Strains from Morus alba and Acer truncatum

by Ruxue Bai, Qingchun Wang and Haiying Bao

J. Fungi 2025, 11(5), 346; https://doi.org/10.3390/jof11050346 (registering DOI) - 29 Apr 2025

Abstract

Inonotus hispidus growing on Morus alba is traditionally regarded as the authentic source of the medicinal fungus. However, this species is also found on other host trees, such as Ulmus macrocarpa and Acer truncatum; yet, whether these strains share comparable genomic and functional traits with Morus-derived strains remains unknown. Here, we performed whole-genome sequencing of a strain isolated from U. macrocarpa (UMI) using Illumina and PacBio platforms and conducted comparative genomic analysis with strains from M. alba (MAI) and A. truncatum (AMI). Antagonistic interactions were also evaluated via dual-culture confrontation assays. The UMI genome was 36.44 Mb in size, comprising 9097 predicted genes, of which 6991 and 1672 were annotated in the KEGG and COG databases, respectively. SNP analysis revealed 623,498 and 335,343 variants in AMI and MAI, with AMI showing greater genomic variation. Core–pan genome analysis identified 2651 core genes and 1046, 1424, and 1217 strain-specific genes in UMI, AMI, and MAI, respectively. Phenotypic assays demonstrated distinct mycelial growth dynamics and antagonistic behaviors, which likely reflect host-related environmental adaptation. Overall, I. hispidus strains from non-Morus hosts exhibit unique genomic and phenotypic features, providing a valuable basis for resource evaluation, artificial domestication, and the medicinal development of wild Sanghuang strains beyond traditional sources. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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25 pages, 4642 KiB

Open AccessArticle

Harnessing Xylanase Potential in Thermothelomyces fergusii: Insights from Computational and Functional Analysis

by Abdul Waheed, Yi Chen, Ying Su, Yuxin Yan and Gang Liu

J. Fungi 2025, 11(4), 250; https://doi.org/10.3390/jof11040250 - 25 Mar 2025

Viewed by 199

Abstract

Xylanases are crucial for the breakdown of hemicellulose, enabling the conversion of lignocellulosic biomass into fermentable sugars for biofuels and other industrial applications. For the first time, we investigated the biochemical and genetic characteristics of 22 xylanase genes from Thermothelomyces fergusii within glycoside hydrolase (GH) families GH10, GH11, and GH43. Xylanase genes structural diversity clustered the phylogenetic tree into GH10, GH11, GH43-I, and GH43-II groups. Structural analysis revealed that all TfGH10 and TfGH11 genes contained conserved GH domains, with CBM1 present in TfGH10-5 and TfGH11-4. Secondary domains, including CBM35, CBM42, and CBM91, were found in the GH43 gene family. The presence of key glutamic (Glu) and aspartic (Asp) residues in active sites is essential for substrate binding and catalysis. RT-qPCR analysis revealed substrate-dependent gene expression, with peak upregulation on day three in beechwood xylan (BWX) cultures and day two in corncob xylan (CCX) and rice straw (RS) cultures. Consistent with these findings, enzymatic assays demonstrated the highest xylanase activity in BWX-induced cultures, followed by RS and CCX, underscoring the differential regulation of these enzymes in response to distinct hemicellulosic substrates. These findings provide valuable insights into the structural, functional, and regulatory mechanisms of T. fergusii xylanases, facilitating their industrial application. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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39 pages, 8285 KiB

Open AccessArticle

The Three-Dimensional Structure of the Genome of the Dark Septate Endophyte Exophiala tremulae and Its Symbiosis Effect on Alpine Meadow Plant Growth

by Chu Wu, Junjie Fan, Die Hu, Honggang Sun, Guangxin Lu, Yun Wang and Yujie Yang

J. Fungi 2025, 11(4), 246; https://doi.org/10.3390/jof11040246 - 24 Mar 2025

Viewed by 422

Abstract

The establishment of artificial grassland is a good pathway for resolving serious social and economic problems in the Qinghai–Tibet Plateau. Some beneficial indigenous microbes may be used to improve productivity in artificial grassland. The genome of the indigenous dark septate fungus, Exophiala tremulae CICC2537, was sequenced and assembled at the chromosome level using the PacBio sequencing platform, with the assistance of the Hi-C technique for scaffolding, and its 3D genome structures were investigated. The genome size of E. tremulae is 51.903848 Mb, and it contains eight chromosomes. A total of 12,277 protein-coding genes were predicted, and 11,932 genes (97.19%) were annotated. As for the distribution of exon and intron number and the distribution of gene GC and CDS GC, E. tremulae showed similar distribution patterns to the other investigated members of the genus Exophiala. The analysis of carbohydrate-active enzymes showed that E. tremulae possesses the greatest number of enzymes with auxiliary activities and the lowest number of enzymes with carbohydrate-binding modules among the investigated fungi. The total number of candidate effector proteins was 3337, out of which cytoplasmic and apoplastic effector proteins made up 3100 and 163, respectively. The whole genome of E. tremulae contained 40 compartment As and 76 compartment Bs, and there was no significant difference in GC content in its compartment As and Bs. The whole genome of E. tremulae was predicted to contain 155 topologically associating domains (TADs), and their average length was 250,000 bp, but there were no significant differences in the numbers of genes and the GC content per bin localized within the boundaries and interiors of TADs. Comparative genome analysis showed that E. tremulae diverged from Exophiala mesophila about 34.1 (30.0–39.1) Myr ago, and from Exophiala calicioides about 85.6 (76.1–90.6) Myr ago. Compared with all the investigated fungi, the numbers of contraction and expansion gene families in the E. tremulae genome were 13 and 89, respectively, and the numbers of contraction and expansion genes were 14 and 670, respectively. Our work provides a basis for the use of the dark septate fungus in alpine artificial grassland and further research into its symbiosis mechanisms, which may improve the growth of plant species used in the Qinghai–Tibet Plateau. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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20 pages, 5071 KiB

Open AccessArticle

Genomic Insights into Cobweb Disease Resistance in Agaricus bisporus: A Comparative Analysis of Resistant and Susceptible Strains

by Guohui Cheng, Xiaoya An, Yueting Dai, Changtian Li and Yu Li

J. Fungi 2025, 11(3), 200; https://doi.org/10.3390/jof11030200 - 4 Mar 2025

Viewed by 878

Abstract

Agaricus bisporus, a globally cultivated edible fungus, faces significant challenges from fungal diseases like cobweb disease caused by Cladobotryum mycophilum, which severely impacts yield. This study aimed to explore the genetic basis of disease resistance in A. bisporus by comparing the genomes of a susceptible strain (AB7) and a resistant strain (AB58). Whole-genome sequencing of AB7 was performed using PacBio Sequel SMRT technology, and comparative genomic analyses were conducted alongside AB58 and other fungal hosts of C. mycophilum. Comparative genomic analyses revealed distinct resistance features in AB58, including enriched regulatory elements, specific deletions in AB7 affecting carbohydrate-active enzymes (CAZymes), and unique cytochrome P450 (CYP) profiles. Notably, AB58 harbored more cytochrome P450 genes related to fatty acid metabolism and unique NI-siderophore synthetase genes, contributing to its enhanced environmental adaptability and disease resistance. Pan-genome analysis highlighted significant genetic diversity, with strain-specific genes enriched in pathways like aflatoxin biosynthesis and ether lipid metabolism, suggesting distinct evolutionary adaptations. These findings provide valuable insights into the genetic basis underlying disease resistance in A. bisporus, offering a foundation for future breeding strategies to improve fungal crop resilience. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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16 pages, 3749 KiB

Open AccessArticle

Analysis of Whole-Genome for Alternaria Species Identification

by Ying Yang, Yutong Gan, Wenjie Xu, Yuanhao Huang, Tianyi Xin, Rui Tan and Jingyuan Song

J. Fungi 2025, 11(3), 185; https://doi.org/10.3390/jof11030185 - 26 Feb 2025

Viewed by 629

Abstract

The genus Alternaria, functioning as a saprobe, endophyte, and plant pathogen, is widely distributed across various natural and human-impacted environments. Leaf spot and black spot diseases, caused by Alternaria species, are the most prevalent plant diseases within this genus, leading to significant reductions in crop yields and substantial economic losses. To facilitate the timely detection of Alternaria species during the early stages of infection, enable targeted treatments, and mitigate associated damages, we employed a species identification method based on Analysis of whole-GEnome (AGE). We downloaded 148 genomes, including 31 Alternaria species, from the NCBI GenBank database. Through bioinformatics analysis, we constructed a specific-target sequence library and selected a representative sequence per species. The specific target sequences of the seven exemplary Alternaria species were subsequently used for validation and rapid detection, utilizing Sanger sequencing and CRISPR-Cas12a technology, respectively. The results demonstrated that our method accurately identified the target species. Additionally, by combining Enzymatic Recombinase Amplification (ERA) with CRISPR-Cas12a, we achieved rapid and precise identification of genomic DNA samples, with a detection limit as low as 0.01 ng/µL within 30 min. Therefore, AGE proves to be a highly robust and efficient method for the detection of Alternaria species, offering broad potential for various applications. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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19 pages, 5008 KiB

Open AccessArticle

Integrated Multi-Omics Analysis to Investigate the Molecular Mechanisms Underlying the Response of Auricularia heimuer to High-Temperature Stress

by Fang Lu, Xin Sun, Xiaodong Dai, Piqi Zhang, Yinpeng Ma, Yafei Xu, Lei Wang and Jiechi Zhang

J. Fungi 2025, 11(3), 167; https://doi.org/10.3390/jof11030167 - 20 Feb 2025

Cited by 1 | Viewed by 553

Abstract

High-temperature stress is a key factor that reduces the yields of edible fungi. Auricularia heimuer (A. heimuer) is a nutrient-rich edible fungus that is widely cultivated in China. In this study, we analyzed the physiological, transcriptomic, and metabolomic results of A. heimuer (variety “Hei29”) under high-temperature stress. Our findings revealed that high temperatures (30 °C and 35 °C) significantly reduced hyphal growth, increased malondialdehyde content and antioxidant enzyme activity, and enhanced the accumulation of secondary metabolites, such as phenolic compounds and flavonoids. A total of 15 candidate genes potentially responsive to high-temperature stress were identified through transcriptomic analysis, including those involved in regulating antioxidant defense, heat shock response, sugar metabolism, amino acid metabolism, and accumulating secondary metabolites. Metabolomic analysis identified three candidate metabolites potentially responsive to high-temperature stress, including kinetin, flavonoids, and caffeic acid, as well as several metabolic pathways, including nucleotide metabolism, ABC transporters, and cofactor biosynthesis. These mechanisms help mitigate oxidative damage to cellular structures and energy deficits caused by elevated temperatures, enabling the fungus to maintain cellular stability, metabolic function, and growth under heat stress. This study is the first to explore the molecular mechanism of A. heimuer in response to high-temperature stress. The results provide valuable insights into the molecular mechanisms of heat stress tolerance in A. heimuer, highlighting potential targets for developing heat-tolerant strains for industrial application. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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18 pages, 3706 KiB

Open AccessArticle

Comparative Genomic Analysis of Two Monokaryons of Auricularia heimuer Hei29

by Fengli Wang, Chuang Han, Jiechi Zhang, Piqi Zhang, Xiaojia Zhang, Xin Yue, Yanshu Zhao and Xiaodong Dai

J. Fungi 2025, 11(2), 122; https://doi.org/10.3390/jof11020122 - 6 Feb 2025

Cited by 1 | Viewed by 787

Abstract

Auricularia heimuer is a valuable traditional Chinese fungus used as food and medicine. Hei29 is a strain derived from wild A. heimuer through systematic domestication and selection. It has been the primary A. heimuer variety in Northeast China for 30 years and offers the advantages of high yield, good commercial property, and stable traits. This study used protoplast nucleation on Hei29 to produce two amiable and paired monokaryons, Hei29-D1 and Hei29-D2. The genome of Hei29 was sequenced utilizing the Illumina PE150 and PacBio Sequel sequencing platforms. Hei29-D1 and Hei29-D2 had genomic sizes of 47.54 Mb and 47.49 Mb, GC contents of 56.95% and 56.99%, and an N50 of 2.37 Mb and 4.28 Mb, respectively. Hei29’s genome possessed two phytoene synthase (PSY) protein genes, one of which—PSY encoded by g894—has a transmembrane domain. The phylogenetic tree showed that Hei29 shared the closest evolutionary relationship with Auricularia subglabra TFB-10046 SS5. Collinearity analysis showed that the correlation between the two monokaryons was as high as 90.81%. Cluster analysis revealed that Hei29 contains 12,362 core genes, 223 unique genes in Hei29-D1, and 228 unique genes in Hei29-D2. This study is the first to sequence two related and paired monokaryons from A. heimuer, which is critical for fully understanding the genetic composition and information of the characteristic strain of A. heimuer in Northeast China. It establishes the data and theoretical foundation for gene mining, usage, and molecular breeding. It further promotes the genetic breeding and active substance utilization of A. heimuer. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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19 pages, 6703 KiB

Open AccessArticle

Whole-Genome Sequencing and Fine Map Analysis of Pholiota nameko

by Yan He, Bo Liu, Xiaoqi Ouyang, Mianyu He, Hongyan Hui, Bimei Tang, Liaoliao Feng, Min Ren, Guoliang Chen, Guangping Liu and Xiaolong He

J. Fungi 2025, 11(2), 112; https://doi.org/10.3390/jof11020112 - 3 Feb 2025

Viewed by 1029

Abstract

Pholiota nameko (T. Ito) S. Ito and S. Imai is an emerging wild mushroom species belonging to the genus Pholiota. Its unique brown–yellow appearance and significant biological activity have garnered increasing attention in recent years. However, there is a relative lack of research on the biological characteristics and genetics of P. nameko, which greatly limits the potential for an in-depth exploration of this mushroom in the research fields of molecular breeding and evolutionary biology. This study aimed to address that gap by employing Illumina and Nanopore sequencing technologies to perform whole-genome sequencing, de novo assembly, and annotation analysis of the P. nameko ZZ1 strain. Utilizing bioinformatics methods, we conducted a comprehensive analysis of the genomic characteristics of this strain and successfully identified candidate genes associated with its mating type, carbohydrate-active enzymes, virulence factors, pan-genome, and drug resistance functions. The genome of P. nameko ZZ1 is 24.58 Mb in size and comprises 33 contigs, with a contig N50 of 2.11 Mb. A hylogenetic analysis further elucidated the genetic relationship between P. nameko and other Pholiota, revealing a high degree of collinearity between P. nameko and ZZ1. In our enzyme analysis, we identified 246 enzymes in the ZZ1 genome, including 68 key carbohydrate-active enzymes (CAZymes), and predicted the presence of 11 laccases, highlighting the strain’s strong potential for cellulose degradation. We conducted a pan-genomic analysis of five closely related strains of Pholiota, yielding extensive genomic information. Among these, there were 2608 core genes, accounting for 21.35% of the total genes, and 135 dispensable genes, highlighting significant genetic diversity among Pholiota and further confirming the value of pan-genomic analysis in uncovering species diversity. Notably, while we successfully identified the A-mating-type locus, composed of the homeodomain protein genes HD1 and HD2 in ZZ1, we were unable to obtain the B-mating-type locus due to technical limitations, preventing us from acquiring the pheromone receptor of the B-mating-type. We plan to supplement these data in future studies and explore the potential impact of the B-mating-type locus on the current findings. In summary, the genome data of ZZ1 presented in this study are not only valuable resources for understanding the genetic basis of this species, but also serve as a crucial foundation for subsequent genome-assisted breeding, research into cultivation technology, and the exploration of its nutritional and potential medicinal value. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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20 pages, 12169 KiB

Open AccessArticle

Influence of Drying Methods on the Morphological Features, Microstructural Properties, and Antioxidant Performance of Floccularia luteovirens: A Metabolomic Analysis

by Mengjun Xiao, Tao Wang, Chuyu Tang, Min He, Xiaojian Pu, Tingjing Zhao and Yuling Li

J. Fungi 2025, 11(1), 78; https://doi.org/10.3390/jof11010078 - 19 Jan 2025

Viewed by 645

Abstract

Floccularia luteovirens (F. luteovirens) has garnered increasing attention as an ingredient in both the pharmaceutical and food industries. Depending on the drying method, the accumulation of metabolites can greatly affect the quality. This research employed an untargeted metabolomics (LC-MS/MS) strategy to elucidate the similarities and differences in the morphological characteristics, microstructure, antioxidant capacity, and metabolic profiles of F. luteovirens subjected to three distinct drying methods: natural air-drying (YG), oven-drying (HG), and vacuum freeze-drying (DG). Our findings indicated that the color of F. luteovirens samples dried using the YG and HG methods was yellow-brown, exhibiting a high degree of browning, whereas the samples processed by the DG method displayed a golden-yellow hue and a desirable fullness. Regarding microstructure, the F. luteovirens samples from the YG and HG methods exhibited small and unevenly distributed pores, in contrast to the samples from the DG method, which were structurally intact and characterized by large inter-tissue pores. The antioxidant activity exhibited by F. luteovirens samples, which were processed using the DG method, was found to be significantly superior compared to the antioxidant activity of samples dried using two other methods. A correlation analysis indicated a significant link between antioxidant capacity and lipid as well as lipid-like molecules. Metabolomic analysis identified 1617 metabolites across 15 superclasses, with lipids, lipid-like molecules, organic acids and derivatives, and organic heterocyclic compounds being the predominant metabolites in F. luteovirens. Furthermore, KEGG enrichment analysis highlighted 20 pathways, indicating that the metabolism of amino acids could be significantly involved in the metabolic processes linked to the drying of F. luteovirens. This research clarifies how different drying techniques impact the metabolites or metabolic pathways of F. luteovirens, identifying the mechanisms that influence its quality and providing a reference for optimizing its processing and storage. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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24 pages, 8588 KiB

Open AccessArticle

Saprotrophic Wood Decay Ability and Plant Cell Wall Degrading Enzyme System of the White Rot Fungus Crucibulum laeve: Secretome, Metabolome and Genome Investigations

by Alexander V. Shabaev, Olga S. Savinova, Konstantin V. Moiseenko, Olga A. Glazunova and Tatyana V. Fedorova

J. Fungi 2025, 11(1), 21; https://doi.org/10.3390/jof11010021 - 31 Dec 2024

Cited by 1 | Viewed by 906

Abstract

The basidiomycete Crucibulum laeve strain LE-BIN1700 (Agaricales, Nidulariaceae) is able to grow on agar media supplemented with individual components of lignocellulose such as lignin, cellulose, xylan, xyloglucan, arabinoxylan, starch and pectin, and also to effectively destroy and digest birch, alder and pine sawdust. C. laeve produces a unique repertoire of proteins for the saccharification of the plant biomass, including predominantly oxidative enzymes such as laccases (family AA1_1 CAZymes), GMC oxidoreductases (family AA3_2 CAZymes), FAD-oligosaccharide oxidase (family AA7 CAZymes) and lytic polysaccharide monooxygenases (family LPMO X325), as well as accompanying acetyl esterases and loosenine-like expansins. Metabolomic analysis revealed that, specifically, monosaccharides and carboxylic acids were the key low molecular metabolites in the C. laeve culture liquids in the experimental conditions. The proportion of monosaccharides and polyols in the total pool of identified compounds increased on the sawdust-containing media. Multiple copies of the family AA1_1, AA3_2, AA7 and LPMOs CAZyme genes, as well as eight genes encoding proteins of the YvrE superfamily (COG3386), which includes sugar lactone lactonases, were predicted in the C. laeve genome. According to metabolic pathway analysis, the litter saprotroph C. laeve can catabolize D-gluconic and D-galacturonic acids, and possibly other aldonic acids, which seems to confer certain ecological advantages. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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17 pages, 9737 KiB

Open AccessArticle

Nanopore Data-Driven T2T Genome Assemblies of Colletotrichum lini Strains

by Elizaveta A. Sigova, Ekaterina M. Dvorianinova, Alexander A. Arkhipov, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Antoniy M. Kaplun, Yakov V. Bodrov, Valeria A. Pavlova, Elena V. Borkhert, Daiana A. Zhernova, Elena N. Pushkova, Nataliya V. Melnikova and Alexey A. Dmitriev

J. Fungi 2024, 10(12), 874; https://doi.org/10.3390/jof10120874 - 16 Dec 2024

Viewed by 1066

Abstract

Colletotrichum lini is a pathogenic fungus that infects flax and causes significant yield losses. In this study, we assembled the genomes of four highly virulent C. lini strains using the Oxford Nanopore Technologies (ONT, R10.4.1 flow cells) and Illumina platforms. The performance of two tools developed for telomere-to-telomere (T2T) genome assembly was compared: Verkko and Hifiasm. Prior to the assembly, ONT reads were corrected using the HERRO algorithm. Verkko generated genome assemblies of high completeness but low contiguity, while Hifiasm allowed the generation of T2T assemblies. Despite significantly different genome coverage with ONT data (25–100×), four assemblies of equal contiguity were obtained: 53.6–54.7 Mb, ten core chromosomes, and two or three accessory chromosomes. A comparative analysis of different polishing tools showed that at a certain genome coverage with the corrected ONT data (≥35×), the additional polishing of the assembly did not improve its accuracy, even with the Illumina data. An analysis of the genome structures of the four C. lini strains revealed a high similarity between the core chromosomes. Thus, our approach enabled assembling T2T Colletotrichum genomes only from the ONT data obtained using R10.4.1 flow cells and may be promising for other fungal genera. These assemblies will allow the accurate identification of strain-specific differences at the chromosome level and will aid in the development of effective strategies to protect flax from anthracnose. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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