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Genetic, Genomics and Big Data Analysis of the Interaction Between...
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Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition

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: closed (10 April 2026) | Viewed by 10880

Special Issue Editors

Prof. Dr. Houxiang Kang

E-Mail Website
Guest Editor
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Interests: genomics; genetics; plant pathology; the application of artificial intelligence in crop breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Zhigang Li

E-Mail Website
Guest Editor
Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou 570228, China
Interests: bioinformatics; computational biology and system biology exploring plant-pathogen interaction; population genetic structure and evolutionary potential
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Wei Li

E-Mail Website
Guest Editor
1. Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
2. College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
Interests: molecular plant–microbe interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue focuses on the genetic, genomics, and big data analysis of the interaction between pathogenic fungi and their hosts. The aim is to explore the intricate relationships between these organisms and uncover valuable insights that can aid in the development of effective strategies for disease management.

This Special Issue plans to bring together a series of research papers that delve into various aspects of this interaction. Starting from the fundamental data of genetics and multi-omics, including genomics, transcriptomics, proteomics, and metabolomics, the aim is to decipher the complex molecular networks at play during the interaction between the host and the pathogen. These analyses provide a holistic view of the complex biological processes and offer potential targets for disease control, considering both the pathogen and the host.

Overall, the main objective of this Special Issue is to provide a comprehensive overview of the genetic, genomics, and big data analysis pertaining to the interaction between pathogenic fungi and plants. The research presented in this Special Issue aims to enhance our understanding of the molecular mechanisms underlying pathogenicity, ultimately offering valuable insights for the development of innovative strategies to effectively combat fungal diseases in agriculture and promote plant health.

Prof. Dr. Houxiang Kang
Dr. Zhigang Li
Prof. Dr. Wei 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

  • genetic
  • genomics
  • big data analysis
  • pathogenic fungi
  • plant–pathogen interaction

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Related Special Issue

Published Papers (7 papers)

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Research

27 pages, 9171 KB  
Article
Whole-Genome Sequencing of Pathogenic Nigrospora musae ST1 Causing Leaf Spot Disease in Idesia polycarpa
by Yun-Ze Chen, Yan Chen and Jing Yang
J. Fungi 2026, 12(3), 226; https://doi.org/10.3390/jof12030226 - 19 Mar 2026
Cited by 1 | Viewed by 681
Abstract
Nigrospora musae ST1 is a newly identified pathogen responsible for leaf spot disease in Idesia polycarpa. In order to further advance our understanding of this strain and improve management strategies for the leaf spot disease, the PacBio Sequel II platform was used [...] Read more.
Nigrospora musae ST1 is a newly identified pathogen responsible for leaf spot disease in Idesia polycarpa. In order to further advance our understanding of this strain and improve management strategies for the leaf spot disease, the PacBio Sequel II platform was used to perform whole-genome sequencing of N. musae ST1. The assembled genome comprised 42 contigs, with a total length of 49,259,803 bp and an average GC content of 56.23%. Functional annotation identified 12,063 protein-coding genes, including 125 Transporter Classification Database (TCDB)-related genes, 3600 pathogen host interaction (PHI) genes, 2503 Virulence Factor Database (DFVF)-related genes, and 722 genes encoding carbohydrate-active enzymes (CAZymes). Integrated analyses of the secretome, PHI, and DFVF databases revealed six secreted carbohydrate-active enzymes implicated in plant pathogenicity, including three glycoside hydrolases, two pectinate lyases, and one cutinase, potentially playing important roles in pathogenicity. A total of 77 secondary metabolite gene clusters were predicted. Comparative genomic analysis between N. musae ST1 and other Nigrospora species revealed differences in genome rearrangements in Nigrospora fungi. In conclusion, this study has clarified the whole-genome structural characteristics and evolutionary relationships of the newly reported pathogenic fungus, N. musae ST1. It provides a theoretical foundation for future investigations into the pathogenic mechanisms of N. musae ST1 infection in I. polycarpa, as well as potential targets for disease control. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition)
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16 pages, 4049 KB  
Article
T2T Colletotrichum lini Genomes with Hifiasm: ONT R9 and R10 Read Processing and Assembly Guidelines for Fungi
by Elizaveta A. Ivankina, Ekaterina M. Dvorianinova, Alexander A. Arkhipov, Antoniy M. Kaplun, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Nikolai M. Barsukov, Olesya D. Moskalenko, Fedor D. Kostromskoy, Kirill A. Klimov, Andrei A. Artamonov, Elena V. Borkhert, Daiana A. Krupskaya, Elena N. Pushkova, Nataliya V. Melnikova and Alexey A. Dmitriev
J. Fungi 2026, 12(1), 45; https://doi.org/10.3390/jof12010045 - 7 Jan 2026
Viewed by 994
Abstract
The assembly of telomere-to-telomere (T2T) genomes is essential for understanding genomic architecture, especially in fungal pathogens with complex karyotypes, such as Colletotrichum lini, causing flax anthracnose disease. This study provides optimized guidelines for the T2T genome assembly using Oxford Nanopore Technologies (ONT) [...] Read more.
The assembly of telomere-to-telomere (T2T) genomes is essential for understanding genomic architecture, especially in fungal pathogens with complex karyotypes, such as Colletotrichum lini, causing flax anthracnose disease. This study provides optimized guidelines for the T2T genome assembly using Oxford Nanopore Technologies (ONT) R9.4.1 and R10.4.1 sequencing data processed with the Hifiasm 0.25.0 assembler (with --ont module). We analyzed ONT sequencing data for four C. lini strains and compared basecalling tools (Guppy and Dorado), read filtration strategies (quality thresholds Q10/Q15 and length cut-offs 5 kb/10 kb), and genome coverage levels from 5× to 160×. Our results demonstrated that Dorado-basecalled reads consistently had higher average quality, especially the R10.4.1 data, leading to improved telomere resolution and complete mitochondrial genome assembly. Moderate genome coverage (40–65×) combined with Q15 quality and 5 kb length filtration for R10.4.1 data, or Q10 and 5 kb for R9.4.1 data, produced the most contiguous and complete assemblies. Overfiltration of reads by length and quality or conversely excessive coverage (>90×) reduced assembly quality, causing fragmentation or erroneous chromosome merging. With optimized parameters of ONT R9.4.1 and R10.4.1 sequencing data preprocessing, Hifiasm efficiently generated T2T and near-T2T assemblies of C. lini genomes: 53.7–56.1 Mb length, 13–30 contigs, 12–13 chromosomes (including 3–12 T2T chromosomes), complete mitochondrial genome, and >98.5% BUSCO completeness. These findings provide a solid framework for ONT-based fungal genome assembly, facilitating future research on genomic variation and pathogenicity in Colletotrichum and related genera. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition)
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11 pages, 1782 KB  
Article
Investigating the Potential Involvement of Glutathione S-Transferases in Defence Against Powdery Scab in Potato
by Sadegh Balotf, Richard Wilson and Calum Wilson
J. Fungi 2025, 11(9), 654; https://doi.org/10.3390/jof11090654 - 4 Sep 2025
Cited by 3 | Viewed by 1334
Abstract
Glutathione S-transferases (GSTs) are key enzymes in plant defences involved in detoxification, redox regulation, and the modulation of secondary metabolism, playing essential roles in the response to pathogen infections. Despite prior genome-wide predictions of GSTs in potato, little is known about their specific [...] Read more.
Glutathione S-transferases (GSTs) are key enzymes in plant defences involved in detoxification, redox regulation, and the modulation of secondary metabolism, playing essential roles in the response to pathogen infections. Despite prior genome-wide predictions of GSTs in potato, little is known about their specific roles in defending against Spongospora subterranea. This study re-analyses our previously generated transcriptomics and proteomics datasets to explore the role of GSTs in two contrasting potato cultivars, ‘Iwa’ (susceptible) and ‘Gladiator’ (resistant), after inoculation with S. subterranea. A total of 69 and 41 GSTs were identified in the transcriptomics and proteomics data, respectively. The majority of these GSTs were upregulated in the resistant cultivar but not in the susceptible cultivar. The upregulation of GSTs in ‘Gladiator’ suggests a more efficient antioxidant and detoxification response following S. subterranea infection. Chromosomal mapping revealed a high number of GSTs on chromosome 9, suggesting a hotspot for GSTs in the potato genome. This research provides direct evidence of the potential involvement of GSTs in resistance to S. subterranea, offering insights into potential targets for breeding resistant potato cultivars. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition)
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15 pages, 2359 KB  
Article
Trichoderma harzianum Cellobiohydrolase Thph2 Induces Reactive Oxygen Species-Mediated Resistance Against Southern Corn Leaf Blight in Maize
by Bo Lang, Hongyi Liu, Gaoyue Si, Xifen Zhang, Cheng Zhang, Jing Wang and Jie Chen
J. Fungi 2025, 11(9), 629; https://doi.org/10.3390/jof11090629 - 27 Aug 2025
Cited by 1 | Viewed by 1209
Abstract
The pathogenic plant fungus Bipolaris maydis is responsible for southern corn leaf blight (SCLB), a widespread agricultural disease that significantly reduces maize yield in various agroecological zones. The present research focuses on characterizing the role of Trichoderma harzianum cellobiohydrolase (CBH) Thph2 in induced [...] Read more.
The pathogenic plant fungus Bipolaris maydis is responsible for southern corn leaf blight (SCLB), a widespread agricultural disease that significantly reduces maize yield in various agroecological zones. The present research focuses on characterizing the role of Trichoderma harzianum cellobiohydrolase (CBH) Thph2 in induced maize resistance to SCLB by triggering the production of reactive oxygen species (ROS) in leaves. First of all, we demonstrated the potential activities of Thph2 in triggering ROS burst and PDC in a model plant, Nicotiana benthamiana. Cell death, ROS burst, and programmed cell death (PCD) were observed in N. benthamiana leaves following transient expression of Thph2, indicating its defensive role against Sclerotinia sclerotiorum infection. The removal of the signal peptide from Thph2 resulted in the complete loss of the cell death phenotype and the accumulation of reactive oxygen species (ROS), confirming that Thph2 functions as a microbial elicitor that primes host plant immunity through ROS-mediated signaling, thereby inducing systemic resistance (ISR). Furthermore, the Thph2 protein conferred resistance against B. maydis in maize, significantly increasing reactive oxygen species (ROS) accumulation (1.5-fold compared to the control) at 48 h post-inoculation (hpi),and leading to the reduction in the lesion area of SCLB by 15.9% at 2 days post-inoculation (dpi). Our results demonstrated that the Thph2 protein markedly enhanced the expression of lox5, aos, and hpl in maize leaves, thereby confirming its function in triggering plant defense mechanisms primarily via the jasmonic acid signaling pathway. This research reveals new molecular mechanisms by which T. harzianum enhances plant defense and showcases the biocontrol efficacy of Thph2 against southern corn leaf blight (SCLB). Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition)
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20 pages, 5739 KB  
Article
Pathogenic Roles of Polyketide Synthase CLPKS18 and (R)-(-)-Mellein from Curvularia lunata in Maize Leaf Spot
by Zhixiang Lu, Lin Shang, Shaoqing Wang, Xinhua Wang, Yaqian Li, Shunping Zhang, Jing Wang and Jie Chen
J. Fungi 2025, 11(9), 627; https://doi.org/10.3390/jof11090627 - 26 Aug 2025
Viewed by 1035
Abstract
Curvularia lunata (Wakkre) Boedijn is an important pathogenic fungus that causes maize leaf spot, a prevalent disease that caused significant yield losses in maize-growing areas in China in the 1990s. Clpks18, a polyketide synthase (CLPKS18) gene, has been identified as a crucial [...] Read more.
Curvularia lunata (Wakkre) Boedijn is an important pathogenic fungus that causes maize leaf spot, a prevalent disease that caused significant yield losses in maize-growing areas in China in the 1990s. Clpks18, a polyketide synthase (CLPKS18) gene, has been identified as a crucial virulence-related gene in C. lunata. However, the impact of Clpks18 and its biosynthesized virulence factor (R)-(-)-mellein on the expression of maize genes related to the defense signal pathway has never been determined. In this study, it was found that Clpks18 and (R)-(-)-mellein significantly interfere with the signaling pathways of JA and IAA in maize leaves but in different ways and in a time-dependent manner. While CLPKS18 inhibited the maize’s JA and IAA signaling pathways through its related secondary metabolite, (R)-(-)-mellein inhibited the JA signaling pathway but stimulated IAA accumulation in maize leaves. In summary, understanding this novel virulence effector’s mechanism of interference with maize resistance enriches the pathology of Curvularia leaf spot in maize on the one hand and provides a foundation for screening the resistance germplasm and chemical fungicides against the disease on the other. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition)
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14 pages, 2745 KB  
Article
Genomic Insights into Neofusicoccum laricinum: The Pathogen Behind Chinese Larch Shoot Blight
by Jialiang Pan, Zhijun Yu, Wenhao Dai, Chunhe Lv, Yifan Chen, Hong Sun, Jie Chen and Junxin Gao
J. Fungi 2025, 11(5), 399; https://doi.org/10.3390/jof11050399 - 21 May 2025
Cited by 2 | Viewed by 1235
Abstract
Larch shoot blight, caused by the fungus Neofusicoccum laricinum, threatens larch (Larix spp.) forests across northeastern China, jeopardizing both timber productivity and ecological stability. This study aimed to investigate the genomic diversity, population structure, and potential adaptive mechanisms of N. laricinum [...] Read more.
Larch shoot blight, caused by the fungus Neofusicoccum laricinum, threatens larch (Larix spp.) forests across northeastern China, jeopardizing both timber productivity and ecological stability. This study aimed to investigate the genomic diversity, population structure, and potential adaptive mechanisms of N. laricinum across contrasting climatic regions. To achieve this, we conducted whole-genome resequencing of 23 N. laricinum isolates collected from three major provinces—Heilongjiang, Inner Mongolia, and Jilin—that represent distinct climatic zones ranging from cold-temperate to relatively warmer regions. We identified ~219.1 K genetic variants, offering a detailed portrait of the pathogen’s genomic diversity. Population structure analyses, including principal component analysis and phylogenetic tree, revealed clear genetic differentiation aligning with geographic origin and climate. Functional annotation (GO and KEGG) highlighted enrichment in metabolic, stress-response, and membrane transport pathways, suggesting potential adaptation to varied temperature regimes and environmental pressures. Moreover, region-specific variants—particularly missense and stop-gain mutations—were linked to genes involved in ATP binding, oxidoreductase activity, and cell division, underscoring the fungus’s capacity for rapid adaptation. Collectively, these findings fill a critical gap in the population genetics of N. laricinum and lay a foundation for future disease management strategies to larch shoot blight under changing climatic conditions. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition)
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13 pages, 5005 KB  
Article
FGSE02, a Novel Secreted Protein in Fusarium graminearum FG-12, Leads to Cell Death in Plant Tissues and Modulates Fungal Virulence
by Zhigang Hao, Lei Pan, Jiaqing Xu, Chengxuan Yu, Jianqiang Li and Laixin Luo
J. Fungi 2025, 11(5), 397; https://doi.org/10.3390/jof11050397 - 21 May 2025
Viewed by 3572
Abstract
Fungal phytopathogens employ effector proteins and secondary metabolites to subvert host immunity. Effector proteins have attracted widespread interest in infection, especially for unknown, unreported genes. However, the type of protein remains much less explored. Here, we combined transcriptome analysis and functional validation to [...] Read more.
Fungal phytopathogens employ effector proteins and secondary metabolites to subvert host immunity. Effector proteins have attracted widespread interest in infection, especially for unknown, unreported genes. However, the type of protein remains much less explored. Here, we combined transcriptome analysis and functional validation to identify virulence-associated genes in Fusarium graminearum during fungi infection. A unique secreted protein, FGSE02, was significantly upregulated in the early infection stage. Proteomic characterization revealed that the protein contains a functional signal peptide but lacks known domains. The transient expression of FGSE02 in Nicotiana benthamiana induced rapid cell death, while gene knockout stains reduced fungal virulence without affecting growth. Our findings highlight FGSE02 as a key virulence factor, offering potential targets for disease control. Taken together, the results of this study identify a pathogenic factor and provide new insights into the development of green pesticides. Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition)
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