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Fungal Metabolomics and Genomics
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Fungal Metabolomics and Genomics

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 2125

Special Issue 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
Dr. Jianzhao Qi

E-Mail Website
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

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 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

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 100 words) can be sent to the Editorial Office for announcement on this website.

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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Published Papers (4 papers)

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Research

19 pages, 6703 KiB  
Article
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 139
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 [...] Read more.
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  
Article
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 380
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 [...] Read more.
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  
Article
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
Viewed by 608
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. [...] Read more.
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  
Article
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 747
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 [...] Read more.
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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