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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 August 2026 | Viewed by 4190

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Special Issue Editors

Prof. Dr. Yuqi Qin

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Guest Editor

National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
Interests: fungal genetics; transcription factors; transcriptional regulation; lignocellulose-degrading enzymes; enzyme production; synthetic biology

Prof. Dr. Jian Zhao

E-Mail Website
Guest Editor

Microbial Technology Institute, Shandong Univeristy, Qingdao 266237, China
Interests: lignocellulose-degrading enzymes; enzyme production; microorganisms producing cellulases, hemicellulases, pectinases, etc., and their engineering modification; pretreatment and fractionation of lignocellulisc biomass; degradation and bioconversion of lignocellulosic biomass; lignocellulose-based sugar platforms; nanocellulose and its application; enzymatic degumming of bast fibers; functional utilization of lignocellulosic biomass
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Dear Colleagues,

Fungi, as one of the most widely distributed and functionally diverse biological groups on Earth, play key roles in ecological balance, industrial production, and human health. Fungal genetics and functional genomics research provide a theoretical foundation and technical support for the precise modification of fungal characteristics by elucidating gene functions and regulatory mechanisms. In recent years, breakthroughs in gene editing, multi-omics integration, and high-throughput functional screening have enabled researchers to efficiently explore fungal secondary metabolites, develop novel enzyme systems, optimize cellular factories, and accelerate the discovery of antifungal drug targets. These advances have significantly promoted innovative applications of fungi in biomanufacturing, pharmaceutical development, fungal biocontrol, and environmental remediation. This Special Issue focuses on progress in fungal genetics and functional genomics. We invite authors to contribute original research or review articles. Potential topics include, but are not limited to, the following areas:

Fungal growth, reproduction, morphogenesis, and differentiation;
Secondary metabolite biosynthesis;
Production, characteristics, and application of fungal enzymes;
Gene function and regulation;
Secretory pathways;
Pathogenicity and host interaction;
Gene editing;
Synthetic biology.

Prof. Dr. Yuqi Qin
Prof. Dr. Jian Zhao
Guest Editors

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Keywords

enzymes
fungal genetics
fungi
gene editing
regulation
secondary metabolites
synthetic biology
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Research

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22 pages, 12165 KB

Open AccessArticle

Mitochondrial Graph-Based Pan-Genome Analysis of Hypsizygus marmoreus: Structural Variation, Adaptive Evolution, and Its Implications for Germplasm Resource Improvement

by Ruichen Ma, Wenyun Li, Yongmei Miao, Ruiheng Yang, Youran Shao, Junjun Shang, Yan Li, Yuan Gao, Dapeng Bao and Yingying Wu

Int. J. Mol. Sci. 2026, 27(7), 3129; https://doi.org/10.3390/ijms27073129 - 30 Mar 2026

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Abstract

Mitochondria regulate nuclear genomes and their own genetic material, primarily to provide energy in eukaryotes. Currently, high-throughput sequencing technologies are being used to resolve the mitochondrial genomes of various edible fungi. However, the application of pan-genomes for the analysis of edible mushroom mitochondrial genomes remains unexplored. In this study, we conducted a comparative mitochondrial genome analysis of 31 Hypsizygus marmoreus strains (four newly sequenced monotypes and 27 public datasets), ranging from 98,284 to 111,087 bp. This variation was determined to be primarily driven by dynamic changes in non-coding regions, particularly intronic polymorphisms in the cox1 gene. Further, transfer RNA (tRNA) secondary structures exhibited atypical globular and elongated conformations alongside copy number variations. Additionally, codon usage showed a pronounced A/T bias, whereas core respiratory chain genes demonstrated an evolutionary pattern of strong purifying selection. Furthermore, the 31 mitochondrial genomes of H. marmoreus were found to harbor eight gene rearrangement patterns and five genetic clusters, and the pan-genome analysis (220,364 bp, 217 nodes) captured abundant single-nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and structural variations. This study provides breeding-relevant genetic markers and a genomic framework for H. marmoreus germplasm classification, genetic improvements, and the molecular breeding of stress-resilient varieties. Full article

(This article belongs to the Special Issue Fungal Genetics and Functional Genomics Research)

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22 pages, 11352 KB

Open AccessArticle

Functional Characterization of a Signal Peptide Peptidase in Phaffia rhodozyma Reveals a Potential Role in Protein Stress Response but Not in Activation of the SREBP Ortholog Sre1

by Marcelo Baeza, Melissa Gómez, Gabriela Apariz, Salvador Barahona and Jennifer Alcaíno

Int. J. Mol. Sci. 2026, 27(6), 2628; https://doi.org/10.3390/ijms27062628 - 13 Mar 2026

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Abstract

Sterol regulatory element-binding proteins (SREBPs) regulate lipid homeostasis and coordinate sterol metabolism and carotenogenesis in the astaxanthin-producing yeast Phaffia rhodozyma. While Sre1, the SREBP ortholog, and the site-2 protease Stp1 have been identified as essential components of this pathway in P. rhodozyma, additional factors involved in Sre1 processing or regulation remain unknown. In Aspergillus species, a signal peptide peptidase contributes to the activation of the SREBP ortholog, raising the possibility of a similar role in this yeast. In this work, we identified and characterized the P. rhodozyma signal peptide peptidase (SppA) homolog. Sequence analysis, domain prediction, and phylogenetic analyses supported its classification within the SPP family of intramembrane aspartyl proteases. To evaluate its functional role, ΔsppA mutants were constructed in genetic backgrounds with constitutive Sre1 activity, including the cyp61⁻ mutant and a strain expressing the active form of Sre1 (Sre1N). Deletion of SPPA did not alter sensitivity to clotrimazole or cobalt chloride, nor affect pigmentation, indicating that SppA is not required for Sre1 activation in P. rhodozyma. Transcriptomic analyses further showed that expression of SRE1 and of its known target genes remained unchanged upon SPPA deletion. Interestingly, the loss of SppA in the Sre1N background caused marked downregulation of genes associated with protein refolding and unfolded protein binding. In agreement with these transcriptional changes, the Sre1NΔsppA strain displayed increased sensitivity to dithiothreitol. These findings suggest that, although SppA is not involved in Sre1 activation in P. rhodozyma, it may play a role in protein stress-related processes. Future studies will be required to define the molecular mechanisms underlying this role and its integration with protein homeostasis networks. Full article

(This article belongs to the Special Issue Fungal Genetics and Functional Genomics Research)

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20 pages, 3137 KB

Open AccessArticle

The Transcription Factor PoCon7 Is Essential for Fungal Viability and Regulates Chitinase Gene Expression in Penicillium oxalicum

by Kexuan Ma, Haiyi Yuan, Jian Zhao and Yuqi Qin

Int. J. Mol. Sci. 2026, 27(1), 333; https://doi.org/10.3390/ijms27010333 - 28 Dec 2025

Viewed by 617

Abstract

The dynamic remodeling of the fungal cell wall depends on a balance between chitin synthesis and degradation. Chitinases are critical for nutrient acquisition, cell wall remodeling, and defense; yet, the upstream regulatory mechanisms controlling chitinase gene expression remain poorly understood. Here, Tandem Affinity Purification–Mass Spectrometry (TAP–MS) with the Penicillium oxalicum Snf1 kinase (PoSnf1) as bait identified the zinc finger transcription factor (TF) PoCon7 as a putative target of the Snf1 kinase complex. This complex comprises the catalytic α subunit Snf1, one of three alternative β subunits Gal83, and the γ subunit Snf4. Although PoCon7 does not directly bind PoSnf1 or PoSnf4, it specifically interacts with PoGal83. Phylogenetic analysis indicates that PoCon7 is a conserved, nuclear-localized C2H2-type TF in filamentous fungi. PoCon7 is likely essential for fungal viability, as only a truncated mutant (con7-B) could be generated, while full deletion was lethal. The con7-B mutant displayed delayed hyphal extension, reduced conidiation, downregulation of developmental genes, and upregulation of cell wall-degrading enzyme (CWDE) genes. DNA Affinity Purification Sequencing (DAP-seq) revealed that PoCon7 binds target gene promoters via the motif 5′-TATTWTTAT-3′. ChIP-qPCR confirmed PoCon7 enrichment at specific sites within the chitinase genes chi18A and chi18C, and the disruption of PoCon7 markedly reduced their expression. Thus, PoCon7 represents the first TF shown to directly regulate chitinase gene expression in filamentous fungi. Full article

(This article belongs to the Special Issue Fungal Genetics and Functional Genomics Research)

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21 pages, 2774 KB

Open AccessArticle

Comparative Transcriptomic Analyses Reveal Potential Stp1 Regulatory Roles Independent of Sre1 in Phaffia rhodozyma

by Marcelo Baeza, Melissa Gómez, Salvador Barahona, Maximiliano Coche-Miranda, Gabriela Apariz and Jennifer Alcaíno

Int. J. Mol. Sci. 2025, 26(24), 12008; https://doi.org/10.3390/ijms262412008 - 13 Dec 2025

Cited by 2 | Viewed by 514

Abstract

Sterol regulatory element-binding proteins (SREBPs) regulate lipid homeostasis in mammals via sequential activation by the site-1 (S1P) and site-2 (S2P) proteases. In the yeast Phaffia rhodozyma, homologs of SREBP (Sre1) and S2P (Stp1) were identified, with Sre1 cleaved by Stp1 and involved in the regulation of sterol and carotenoid biosynthesis. Additional regulatory roles of S2P have been described in other organisms, but such functions remain unexplored in P. rhodozyma, a question addressed in this study. Transcriptomic analyses of Δsre1, Δstp1, and Δsre1Δstp1 mutants were performed in both wild-type and Sre1-activated conditions. Potential genes regulated by Stp1 independently of Sre1 were identified, and their cellular roles were determined by KEGG mapping and Gene Ontology classification. As expected, most transcriptional changes in Δstp1 mutants reflected Sre1-mediated regulation. Notably, a subset of genes displayed differential expression independently of Sre1. These genes were linked to diverse aspects of cellular homeostasis, including metabolism, protein folding, ER stress response, and ribosome biogenesis. The transcriptomic analysis suggests that Stp1 regulates gene expression beyond the Sre1 transcription factor in P. rhodozyma, providing a framework for future studies to confirm and further explore these functions. Full article

(This article belongs to the Special Issue Fungal Genetics and Functional Genomics Research)

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Review

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30 pages, 1039 KB

Open AccessReview

Molecular Identification and RNA-Based Management of Fungal Plant Pathogens: From PCR to CRISPR/Cas9

by Rizwan Ali Ansari, Younes Rezaee Danesh, Ivana Castello and Alessandro Vitale

Int. J. Mol. Sci. 2026, 27(2), 1073; https://doi.org/10.3390/ijms27021073 - 21 Jan 2026

Viewed by 1638

Abstract

Fungal diseases continue to limit global crop production and drive major economic losses. Conventional diagnostic and control approaches depend on time-consuming culture-based methods and broad-spectrum chemicals, which offer limited precision. Advances in molecular identification have changed this landscape. PCR, qPCR, LAMP, sequencing and portable platforms enable rapid and species-level detection directly from plant tissue. These tools feed into RNA-based control strategies, where knowledge of pathogen genomes and sRNA exchange enables targeted suppression of essential fungal genes. Host-induced and spray-induced gene silencing provide selective control without the long-term environmental costs associated with chemical use. CRISPR/Cas9 based tools now refine both diagnostics and resistance development, and bioinformatics improves target gene selection. Rising integration of artificial intelligence indicates a future in which disease detection, prediction and management connect in near real time. The major challenge lies in limited field validation and the narrow range of fungal species with complete molecular datasets, yet coordinated multi-site trials and expansion of annotated genomic resources can enable wider implementation. The combined use of molecular diagnostics and RNA-based strategies marks a shift from disease reaction to disease prevention and moves crop protection towards a precise, sustainable and responsive management system. This review synthesizes the information related to current molecular identification tools and RNA-based management strategies, and evaluates how their integration supports precise and sustainable approaches for fungal disease control under diverse environmental settings. Full article

(This article belongs to the Special Issue Fungal Genetics and Functional Genomics Research)

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