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Advances in Genomics of Pathogenic Fungi
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Advances in Genomics of Pathogenic Fungi

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: 15 June 2025 | Viewed by 7787

Special Issue Editors

Dr. Nicomedes Valenzuela-Lopez

E-Mail Website
Guest Editor
Unidad de Microbiología, Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta, Chile
Interests: fungi; genomics; pathogenic fungi; fungal infection; mycology
Dr. Benito Gomez-Silva

E-Mail Website
Guest Editor
Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
Interests: extreme environments; microbiology; cyanobacteria; algae; Atacama Desert
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Fungi are a diverse and large group of eukaryotes. They are distributed across all different ecological niches, such as aquatic and terrestrial environments, adapting their lives to a variety of stressful conditions, including frozen areas and deserts, high UV radiation and desiccation. A group of these fungi impact the health of plants, animals, and humans. Different fungal forms, such as mushrooms, molds and yeasts, can be toxic or pathogenic to humans, plants, animals, and other organisms.

Recently, the World Health Organization (WHO) released a guide with the fungal priority pathogens in order to develop public health actions. On the other hand, several fungi are plant pathogens causing significant economic losses in crops worldwide. Studies on the genes involved in the pathogenicity of these organisms are key for understanding their mechanisms of infection and implementing new strategies for control.

This Special Issue attempts to capture research on the genomics of pathogenic fungi. We welcome submissions on all groups of fungi (yeasts, mushrooms, plant fungal pathogens, human fungal pathogens, etc.). Both original research papers and review papers are welcome. Our focus will be on studies using multiple molecular approaches in fungal genomics.

Dr. Nicomedes Valenzuela-Lopez
Dr. Benito Gomez-Silva
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. Genes 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

  • fungal genomics
  • molds
  • yeasts
  • mushrooms
  • pathogenic fungi
  • fungal genes
  • mycology

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Published Papers (4 papers)

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Research

11 pages, 2790 KiB  
Article
The Antidepressant Sertraline Modulates Gene Expression and Alternative Splicing Events in the Dermatophyte Trichophyton rubrum: A Comprehensive Analysis
by Carlos H. Lopes Rocha, Flaviane M. Galvão Rocha, Pablo R. Sanches, Antonio Rossi and Nilce M. Martinez-Rossi
Genes 2025, 16(2), 146; https://doi.org/10.3390/genes16020146 - 24 Jan 2025
Viewed by 805
Abstract
Background/Objectives: Dermatophytosis, a prevalent fungal infection of keratinized tissues, is primarily caused by the filamentous fungus Trichophyton rubrum. Sertraline (SRT), an antidepressant with antifungal activity, has already demonstrated therapeutic potential against this fungus. Elucidating the effects of SRT may provide insights into [...] Read more.
Background/Objectives: Dermatophytosis, a prevalent fungal infection of keratinized tissues, is primarily caused by the filamentous fungus Trichophyton rubrum. Sertraline (SRT), an antidepressant with antifungal activity, has already demonstrated therapeutic potential against this fungus. Elucidating the effects of SRT may provide insights into its mechanism of action and fungal adaptation to this drug. Differential gene expression and alternative splicing (AS) facilitate fungal adaptations to various environmental conditions. This study aimed to provide a comprehensive overview of AS events and their implications in T. rubrum cultivated under sub-inhibitory concentrations of SRT. Method: The transcriptome of T. rubrum challenged with SRT was analyzed to detect AS events. Results: RNA-seq analysis revealed that SRT affected transcriptional and post-transcriptional events in numerous T. rubrum genes, including those encoding transcription factors, kinases, and efflux pumps. Among the AS events, intron retention was predominant. After 12 h of SRT exposure, intron-3 retention levels in the serine/arginine protein kinase mRNA transcripts were significantly increased compared with those in the control. This new isoform would produce a putative protein that partially lost its phosphotransferase domain. Conclusions: These findings highlight the potential mechanisms of action of SRT and suggest how T. rubrum adapts itself to this drug. Full article
(This article belongs to the Special Issue Advances in Genomics of Pathogenic Fungi)
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17 pages, 4068 KiB  
Article
Genomic and Pathogenic Characterization of Akanthomyces muscarius Isolated from Living Mite Infesting Hazelnut Big Buds
by Silvia Turco, Mounira Inas Drais, Luca Rossini, Nicolò Di Sora, Federico Brugneti, Stefano Speranza, Mario Contarini and Angelo Mazzaglia
Genes 2024, 15(8), 993; https://doi.org/10.3390/genes15080993 - 28 Jul 2024
Cited by 3 | Viewed by 1287
Abstract
The capability of entomopathogenic fungi to live as plant endophytes is well established. However, their presence in undiscovered environmental niches represents the beginning of a new challenging research journey. Recently, Akanthomyces muscarius (Ascomycota, Cordycipitaceae) (Petch) Spatafora, Kepler & B. Shrestha was isolated from [...] Read more.
The capability of entomopathogenic fungi to live as plant endophytes is well established. However, their presence in undiscovered environmental niches represents the beginning of a new challenging research journey. Recently, Akanthomyces muscarius (Ascomycota, Cordycipitaceae) (Petch) Spatafora, Kepler & B. Shrestha was isolated from hazelnut buds infested by the big bud mite pest Phytoptus avellanae Nalepa, which makes the buds swollen, reddish, and unable to further develop. Gall formation is known to be regulated by a consortium of microbes and mites, and to better understand the possible role of A. muscarius within the infested gall, its whole genome sequence was obtained using a hybrid approach of Illumina and Nanopore reads. The functional and comparative genomics analysis provided within this study may help answer questions related to the ecology and the entomopathogenicity of this fungus. Full article
(This article belongs to the Special Issue Advances in Genomics of Pathogenic Fungi)
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18 pages, 3056 KiB  
Article
Assessment of Candidate Reference Genes for Gene Expression Studies Using RT-qPCR in Colletotrichum fructicola from Litchi
by Dingming Dong, Rong Huang, Yuzhuan Hu, Xinyan Yang, Dagao Xu and Zide Jiang
Genes 2023, 14(12), 2216; https://doi.org/10.3390/genes14122216 - 14 Dec 2023
Cited by 5 | Viewed by 1976
Abstract
Litchi (Litchi chinensis Sonn.) is a tropical fruit originating from southern China that is currently cultivated in subtropical and tropical regions worldwide. Litchi anthracnose, caused by Colletotrichum fructicola, a dominant species of Colletotrichum spp., is an important disease of litchi that damages [...] Read more.
Litchi (Litchi chinensis Sonn.) is a tropical fruit originating from southern China that is currently cultivated in subtropical and tropical regions worldwide. Litchi anthracnose, caused by Colletotrichum fructicola, a dominant species of Colletotrichum spp., is an important disease of litchi that damages the fruits in fields and in post-harvest storage. Real-time quantitative PCR (RT-qPCR) is a common technique with which to detect the expression of and function of target genes quickly and precisely, and stable reference genes are crucial. However, there is no comprehensive information on suitable reference genes of C. fructicola present. Here, we designed eight candidate genes (GAPDH, α-tubulin, 18S, β-tubulin, EF1a, TATA, RPS5, and EF3) using RefFinder software (programs: geNorm, ΔCt, BestKeeper, and NormFinder) to investigate their reliability in the detection of C. fructicola under five different treatments (fungal development stage, temperature, UV, culture medium, and fungicide). The results showed the optimal reference genes under different conditions: EF1a and α-tubulin for developmental stage; α-tubulin and β-tubulin for temperature; α-tubulin and RPS5 for UV treatment; RPS5 and α-tubulin for culture medium; α-tubulin, GAPDH, and TATA for fungicide treatments. The corresponding expression patterns of HSP70 (Heat shock protein 70) were significantly different when the most and the least stable reference genes were selected when treated under different conditions. Our study provides the first detailed list of optimal reference genes for the analysis of gene expression in C. fructicola via RT-qPCR, which should be useful for future functional studies of target genes in C. fructicola. Full article
(This article belongs to the Special Issue Advances in Genomics of Pathogenic Fungi)
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10 pages, 8211 KiB  
Article
Improved RAPD Method for Candida parapsilosis Fingerprinting
by Iwona Wojciechowska-Koszko, Magdalena Mnichowska-Polanowska, Paulina Roszkowska, Michał Sławiński, Stefania Giedrys-Kalemba, Barbara Dołęgowska, Monika Sienkiewicz, Beata Hukowska-Szematowicz and Paweł Kwiatkowski
Genes 2023, 14(4), 868; https://doi.org/10.3390/genes14040868 - 5 Apr 2023
Cited by 1 | Viewed by 2876
Abstract
Recently, methods based on the analysis of arbitrarily amplified target sites of genome microorganisms have been extensively applied in microbiological studies, and especially in epidemiological studies. The range of their application is limited by problems with discrimination and reproducibility resulting from a lack [...] Read more.
Recently, methods based on the analysis of arbitrarily amplified target sites of genome microorganisms have been extensively applied in microbiological studies, and especially in epidemiological studies. The range of their application is limited by problems with discrimination and reproducibility resulting from a lack of standardized and reliable methods of optimization. The aim of this study was to obtain optimal parameters of the Random Amplified Polymorphic DNA (RAPD) reaction by using an orthogonal array as per the Taguchi and Wu protocol, modified by Cobb and Clark for Candida parapsilosis isolates. High Simpson’s index values and low Dice coefficients obtained in this study indicated a high level of interspecies DNA polymorphism between C. parapsilosis strains, and the optimized RAPD method proved useful in the microbiological and epidemiological study. Full article
(This article belongs to the Special Issue Advances in Genomics of Pathogenic Fungi)
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