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18 pages, 4594 KB

Open AccessArticle

Colletotrichum fructicola CfGti1 Transcriptionally Regulates Penetration, Colonization, and Pathogenicity on Apple

by Wenkui Liu, Wei Zhang, Wenxin Shi, Yecan Pan, Pengbo Dai, Chen Yang, Yanjie Wang, Mark L. Gleason, Rong Zhang, Guangyu Sun and Bianqing Hao

J. Fungi 2026, 12(1), 36; https://doi.org/10.3390/jof12010036 - 2 Jan 2026

Cited by 1 | Viewed by 707

Abstract

Glomerella leaf spot (GLS), mainly caused by Colletotrichum fructicola, is a destructive disease of apple. However, the underlying pathogenesis mechanisms of GLS are still largely obscure. Previous infection transcriptome analysis showed that transcription factor CfGti1 was induced during leaf infection. The present [...] Read more.

Glomerella leaf spot (GLS), mainly caused by Colletotrichum fructicola, is a destructive disease of apple. However, the underlying pathogenesis mechanisms of GLS are still largely obscure. Previous infection transcriptome analysis showed that transcription factor CfGti1 was induced during leaf infection. The present study confirms that the CfGti1 gene is strongly expressed in conidia and early infection. To identify functions performed, we generated gene deletion mutant ΔCfGti1 by homologous recombination. Phenotypic analysis revealed that ΔCfGti1 lost pathogenicity to apple leaves by blocking appressorium-mediated host penetration, although penetration pegs still developed on cellophane. In addition, ΔCfGti1 colonization and hyphal extension in wounded apple fruit were dramatically decreased. The ΔCfGti1 mutant exhibited defects in growth and development of hyphae, which may be partly responsible for its inability to colonize apple. Comparative transcriptome and qRT-PCR analyses suggested that CfGti1 regulated appressorium-mediated host penetration by modulating genes related to metabolism of appressorial lipid droplets. Interestingly, CfGti1 also regulated the expression of ybtS and AKT1 or AFT1-1 related to biosynthesis of AK and AF host-specific toxins. This study demonstrated that CfGti1 is a pivotal regulator for apple GLS pathogenesis in C. fructicola. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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15 pages, 4015 KB

Open AccessArticle

by Panpan Zhang, Junling Wang, Guojie Li, Shangshang Xiao, Lei Sun, Xiao Li, Jinghua Tian, Ming Li and Shoumian Li

J. Fungi 2025, 11(12), 865; https://doi.org/10.3390/jof11120865 - 5 Dec 2025

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Abstract

A genetic linkage map of Grifola albicans f. huishuhua (Maitake) is an important resource for chromosome analysis and the genetic basis of phenotypic variation determination. A total of 92 monokaryotic isolates were selected from the F1 generation of Q3-8 × Y1-18 in this [...] Read more.

A genetic linkage map of Grifola albicans f. huishuhua (Maitake) is an important resource for chromosome analysis and the genetic basis of phenotypic variation determination. A total of 92 monokaryotic isolates were selected from the F1 generation of Q3-8 × Y1-18 in this study. Restriction site-associated DNA sequencing, as well as identification of single nucleotide polymorphisms (SNPs), was performed, aiming to illustrate a high-density genetic linkage map. A total of 1122 high-quality SNP markers were located on a map with a length of 1473.60 centimorgan (cM) by screening 589534 SNPs. This map covers 12 linkage groups (LGs) with an average genetic distance of 122.80 cM. Three quantitative trait loci (QTLs) related to the growth rate of G. albicans f. huishuhua strains were identified using the composite interval mapping method. These QTLs were mapped to linkage groups (LGs) as follows: LG3 (qmgv), LG4 (qmb), LG5 (qmd), LG8 (qrdm1, qrdm2), and LG10 (qmgrc1, qmgrc2, qmgrc3). The genes associated with mycelial growth rate and biomass production of these strains were identified. This information could be used for molecular marker-assisted selective breeding in G. albicans f. huishuhua. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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19 pages, 1660 KB

Open AccessArticle

Adaptation of the Phytopathogenic Fungus Microdochium nivale to the Fungicides Tebuconazole and Fludioxonil

by Olga A. Gogoleva, Guzalia Sh. Murzagulova, Egor A. Ryazanov, Maria I. Antonova, Anastasiya A. Lebedeva, Sergey N. Ponomarev, Mira L. Ponomareva and Vladimir Y. Gorshkov

J. Fungi 2025, 11(12), 859; https://doi.org/10.3390/jof11120859 - 2 Dec 2025

Viewed by 891

Abstract

The study investigated the adaptation of the snow mold causal fungus, Microdochium nivale, to the fungicides fludioxonil and tebuconazole. Analysis of intrapopulation diversity among 136 M. nivale strains from two Russian populations revealed no strains with high-level resistance to these fungicides. However, [...] Read more.

The study investigated the adaptation of the snow mold causal fungus, Microdochium nivale, to the fungicides fludioxonil and tebuconazole. Analysis of intrapopulation diversity among 136 M. nivale strains from two Russian populations revealed no strains with high-level resistance to these fungicides. However, the strains exhibited considerable variability in their sensitivity to small fungicide doses. Fungicide sensitivity levels were not associated with virulence levels, whereas strains from different phylogenetic groups exhibited different predispositions to decreased sensitivity to tebuconazole and fludioxonil. In vitro adaptation experiments were conducted to assess: (1) the potential ability of M. nivale to acquire high-level resistance to these fungicides; (2) the relative adaptation efficiency to each fungicide; and (3) the impact of resistance acquisition on virulence. Our results showed that M. nivale strains could adapt to high concentrations of both fungicides with little or no effect on virulence. Adaptation to fludioxonil was significantly less effective than to tebuconazole. To get closer to understanding the mechanisms of fludioxonil adaptation in M. nivale, whole-genome sequencing was performed on a fludioxonil-adapted derivative and its parental fludioxonil-sensitive strain. Comparative genome analysis identified mutations potentially involved in the enhanced fludioxonil resistance, which are discussed within the framework of molecular resistance mechanisms. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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18 pages, 2520 KB

Open AccessArticle

Population, Physiological, and Genetic Insights into Carbendazim Resistance in Populations of the Phytopathogenic Fungus Microdochium nivale

by Guzalia Sh. Murzagulova, Olga A. Gogoleva, Egor A. Ryazanov, Karina A. Shatravina, Natalia V. Tendiuk, Ildar T. Sakhabutdinov, Sergey N. Ponomarev, Inna B. Chastukhina, Olga N. Makshakova, Mira L. Ponomareva and Vladimir Y. Gorshkov

J. Fungi 2025, 11(9), 639; https://doi.org/10.3390/jof11090639 - 29 Aug 2025

Cited by 1 | Viewed by 1310

Abstract

Fungicide treatment is one of the most common methods for controlling fungal plant diseases. However, many phytopathogenic fungi develop resistance to fungicides. Addressing this agriculturally important issue requires comprehensive investigations into fungicide resistance. Our study aims to assess the degree and prevalence of [...] Read more.

Fungicide treatment is one of the most common methods for controlling fungal plant diseases. However, many phytopathogenic fungi develop resistance to fungicides. Addressing this agriculturally important issue requires comprehensive investigations into fungicide resistance. Our study aims to assess the degree and prevalence of resistance to carbendazim—one of the most widely used fungicides—in populations of Microdochium nivale, the causal agent of the deleterious plant disease pink snow mold; to explore possible relationships between carbendazim resistance and physiological and genetic traits; and to gain insight into the molecular basis of carbendazim resistance in this species. We showed that carbendazim resistance is widespread in the analyzed M. nivale populations, and that the application of carbendazim increases the proportion of resistant strains. Nevertheless, carbendazim-resistant strains are present at high relative abundance in populations that have never been exposed to fungicides. Carbendazim resistance in M. nivale is strongly associated with sequence variations in the β-tubulin gene, resulting in amino acid sequence variability that leads to differential affinity for carbendazim. Additionally, we propose a metabarcoding-based approach employing a genetic marker linked to a specific phenotypic trait to assess the ratio of genotypes with contrasting properties within a particular fungal species in environmental communities. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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21 pages, 11439 KB

Open AccessArticle

CBC Complex Regulates Hyphal Growth, Sclerotial Quantity, and Pathogenicity in the Necrotrophic Fungus Botrytis cinerea

by Yinshan Zhang, Xueting Chen, Guihua Li, Qingming Qin, Mingzhe Zhang and Jianchun Qin

J. Fungi 2025, 11(6), 429; https://doi.org/10.3390/jof11060429 - 2 Jun 2025

Viewed by 1513

Abstract

The cap-binding protein complex (CBC), comprising Cbp20 and Cbp80, is crucial for gene expression, yet its role in the notorious crop pathogen Botrytis cinerea remains unclear. Immunoprecipitation coupled with LC-MS/MS demonstrated that BcCbp20 interacts with BcCbp80. Yeast two-hybrid, GST pull-down, and Split-luciferase complementation [...] Read more.

The cap-binding protein complex (CBC), comprising Cbp20 and Cbp80, is crucial for gene expression, yet its role in the notorious crop pathogen Botrytis cinerea remains unclear. Immunoprecipitation coupled with LC-MS/MS demonstrated that BcCbp20 interacts with BcCbp80. Yeast two-hybrid, GST pull-down, and Split-luciferase complementation assays confirmed that the conserved RNA recognition motif (RRM, 54–127 aa) of BcCbp20 and the N-terminal MIF4G domain (1–370 aa, 1–577 aa) of BcCbp80 constitute the core interaction regions. Genetic transformation experiments revealed that BcCBP80 exerts a more dominant role than BcCBP20 in regulating hyphal morphology, growth rate, conidiophore development, and conidial yield. Furthermore, BcCBP20 and BcCBP80 differentially regulate sclerotium formation to maintain sclerotial quantity. Based on pathogenicity assays, BcCBP80 associated with infection cushion development, with this phenotypic alteration possibly being among the factors correlated with altered pathogenicity. However, the increased sensitivity of ΔBccbp20 to various stress factors may be the primary reason for the diminished pathogenicity. Taken together, these results indicate that BcCBP20 and BcCBP80 play important roles in multiple aspects of B. cinerea growth, development, stress response, and pathogenicity. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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19 pages, 7233 KB

Open AccessArticle

Whole-Genome Sequencing of Flammulina filiformis and Multi-Omics Analysis in Response to Low Temperature

by Xinmin Liang, Jing Han, Yuqin Cui, Xueqin Shu, Mengting Lei, Bo Wang, Dinghong Jia, Weihong Peng, Xiaolan He and Xun Liu

J. Fungi 2025, 11(3), 229; https://doi.org/10.3390/jof11030229 - 17 Mar 2025

Cited by 3 | Viewed by 1984

Abstract

The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon [...] Read more.

The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon and multi-omics data (transcriptome and metabolome) analyses of the mycelia, primordia, and fruiting bodies were conducted in the present study. Genome sequencing based on PacBio HiFi and Hi-C resulted in a 36.3 Mb genome sequence that mapped to 12 chromosomes, comprising 11,886 protein-coding genes. A total of 25 cold-responsive (COR) genes and 520 cold-adapted enzymes were identified in the genome. Multi-omics analyses showed that the pathways related to carbohydrate metabolism in the mycelia under low temperature (10 °C) were significantly enriched. Further examination of the expression profiles of carbohydrate-active enzymes (CAZymes) involved in carbohydrate metabolism revealed that out of 515 CAZyme genes in F. filiformis, 58 were specifically upregulated in mycelia under low-temperature conditions. By contrast, the expression levels of these genes in primordia and fruiting bodies reverted to those prior to low-temperature exposure. These indicate that CAZyme genes are important for the low-temperature adaptation of F. filiformis. This research contributes to the targeted breeding of F. filiformis. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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17 pages, 7327 KB

Open AccessArticle

SsNEP2 Plays a Role in the Interaction Between Sclerotinia sclerotiorum and Coniothyrium minitans

by Huizhang Zhao, Zihang Zhu, Yueli Xu, Haixuan Wang, Jiatao Xie, Jiasen Cheng, Daohong Jiang and Yanping Fu

J. Fungi 2025, 11(2), 151; https://doi.org/10.3390/jof11020151 - 16 Feb 2025

Cited by 2 | Viewed by 1640

Abstract

Sclerotinia sclerotiorum, a fungal pathogen that is spread worldwide and causes serious diseases on crops, can be parasitized specifically by the mycoparasite Coniothyrium minitans. SsNEP2, encoding a necrosis-inducing protein in S. sclerotiorum, was previously inferred to play a role in the [...] Read more.

Sclerotinia sclerotiorum, a fungal pathogen that is spread worldwide and causes serious diseases on crops, can be parasitized specifically by the mycoparasite Coniothyrium minitans. SsNEP2, encoding a necrosis-inducing protein in S. sclerotiorum, was previously inferred to play a role in the virulence to host plants. In this study, silencing of SsNEP2 in S. sclerotiorum had no significant (p < 0.01) influence on mycelial morphology, while overexpression led to lower mycelial growth and more branches. When amended with the fermentation broth of the SsNEP2 silencing mutants, conidial germination of C. minitans was promoted, while conidial production decreased. When parasitized by C. minitans, enhanced resistance of the SsNEP2 silencing mutants and weaker resistance of the overexpressed transformants were observed compared to the wild-type S. sclerotiorum strain 1980. In addition, the expression of SsNEP2 in C. minitans enhanced mycelial parasitism on S. sclerotiorum and restored the effect of silencing SsNEP2 in S. sclerotiorum on mycoparasitism. Thus, we highlight the role of SsNEP2 as a PAMP-like protein in the mycoparasitism between C. minitans and its host fungus S. sclerotiorum. SsNEP2 can be used to promote the biological potential of C. minitans. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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17 pages, 7903 KB

Open AccessArticle

Characterization of Endofungal Bacteria and Their Role in the Ectomycorrhizal Fungus Helvella bachu

by Caihong Wei, Mengqian Liu, Guoliang Meng, Miao Wang, Xin Zhou, Jianping Xu, Jianwei Hu, Lili Zhang and Caihong Dong

J. Fungi 2024, 10(12), 889; https://doi.org/10.3390/jof10120889 - 23 Dec 2024

Cited by 2 | Viewed by 1899

Abstract

Helvella bachu, an ectomycorrhizal fungus, forms a symbiotic relationship with Populus euphratica, a rare and endangered species crucial to desert riparian ecosystems. In this study, endofungal bacteria (EFBs) within the fruiting bodies of H. bachu were confirmed by a polyphasic approach, [...] Read more.

Helvella bachu, an ectomycorrhizal fungus, forms a symbiotic relationship with Populus euphratica, a rare and endangered species crucial to desert riparian ecosystems. In this study, endofungal bacteria (EFBs) within the fruiting bodies of H. bachu were confirmed by a polyphasic approach, including genomic sequencing, real-time quantitative PCR targeting the 16S rRNA gene, full-length and next-generation sequencing (NGS) of the 16S rRNA gene, and culture methods. The genera Stenotrophomonas, Variovorax, Acidovorax, and Pedobacter were abundant in the EFBs of fruiting bodies associated with three Populus hosts and were consistently present across different developmental stages. Notably, S. maltophilia and V. paradoxus were detected in high abundance, as revealed by full-length 16S rRNA sequencing, with S. maltophilia also isolated by culture methods. KO-pathway analysis indicated that pathways related to primary, secondary, and energy metabolism were predominantly enriched, suggesting these bacteria may promote H. bachu growth by producing essential compounds, including sugars, proteins, and vitamins, and secondary metabolites. This study confirmed the presence of EFBs in H. bachu and provided the first comprehensive overview of their structure, functional potential, and dynamic changes throughout fruiting body maturation, offering valuable insights for advancing the artificial domestication of this species. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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