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21 pages, 4962 KiB

Open AccessArticle

Genome Sequencing and Comparative Transcriptomic Analysis of Rice Brown Spot Pathogen Bipolaris oryzae Adaptation to Osmotic Stress

by Chun Wang, Kexin Yang, Sauban Musa Jibril, Ruoping Wang, Chengyun Li and Yi Wang

J. Fungi 2025, 11(3), 227; https://doi.org/10.3390/jof11030227 - 17 Mar 2025

Viewed by 454

Abstract

Rice brown spot disease, caused by Bipolaris oryzae, is a significant fungal disease that poses a major threat to global rice production. Despite its widespread impact, genomic studies of B. oryzae remain limited, particularly those involving high-quality genomic data. In this study, [...] Read more.

Rice brown spot disease, caused by Bipolaris oryzae, is a significant fungal disease that poses a major threat to global rice production. Despite its widespread impact, genomic studies of B. oryzae remain limited, particularly those involving high-quality genomic data. In this study, we performed whole-genome sequencing of the B. oryzae strain RBD1, which was isolated from the demonstration field for upland rice cultivation in Haozhiba Village, Lancang County, Pu’er City, Yunnan Province, China, using a combination of second-generation Illumina sequencing and third-generation Single-Molecule Real-Time (SMRT) sequencing. The assembled genome was 37.5 Mb in size with a G + C content of 49.39%, containing 42 contigs with a contig N50 of 2.0 Mb. Genomic analysis identified genes related to carbon, nitrogen, and lipid metabolism, highlighting the strain’s metabolic flexibility under diverse environmental conditions and host interactions. Additionally, we identified pathogenicity-related genes involved in MAPK signaling, G protein signaling, and oxidative stress responses. Under 1.2 M sorbitol-induced osmotic stress, we observed significant differences in growth responses between RBD1 and the rice blast fungus Magnaporthe oryzae H7. Transcriptomic analysis using Illumina sequencing revealed that RBD1 responds to osmotic stress by enhancing carbohydrate metabolism, fatty acid degradation, and amino acid synthesis, while H7 primarily relies on protein synthesis to enhance growth tolerance. This study provides a valuable foundation for understanding the pathogenic mechanisms of rice brown spot and future disease control strategies. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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17 pages, 3842 KiB

Open AccessArticle

Global Analysis of microRNA-like RNAs Reveals Differential Regulation of Pathogenicity and Development in Fusarium oxysporum HS2 Causing Apple Replant Disease

by Ruxin Zhao, Xiangmin Suo, Xianglong Meng, Yanan Wang, Pengbo Dai, Tongle Hu, Keqiang Cao, Shutong Wang and Bo Li

J. Fungi 2024, 10(12), 883; https://doi.org/10.3390/jof10120883 - 19 Dec 2024

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Abstract

This study investigated the expression profiles of microRNA-like RNAs (milRNAs) in Fusarium oxysporum HS2 (FoHS2), a key pathogen causing Apple replant disease (ARD), across spore to mycelium formation stages. Using small RNA sequencing (sRNA-seq) and bioinformatics, we identified and analyzed milRNAs, [...] Read more.

This study investigated the expression profiles of microRNA-like RNAs (milRNAs) in Fusarium oxysporum HS2 (FoHS2), a key pathogen causing Apple replant disease (ARD), across spore to mycelium formation stages. Using small RNA sequencing (sRNA-seq) and bioinformatics, we identified and analyzed milRNAs, revealing their targeting of 2364 mRNAs involved in 20 functional categories, including metabolic and cellular processes, based on gene ontology (GO) analysis. An analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these mRNAs are related to carbohydrate and amino acid metabolism pathways. Notably, the highest number of differentially or specifically expressed milRNAs (DEmilRNAs/SEmilRNAs) was found during the spore stage, with FoHS2-milR19 targeting genes encoding histone acetyltransferases, methyltransferases, and cell wall-degrading enzymes (CWDEs), which are crucial for growth, development, and pathogenicity. We validated the reliability of our sRNA-seq data and the expression of target genes using stem-loop RT-PCR and qRT-PCR. Our results highlight the stage-specific expression of milRNAs in FoHS2, particularly in the spore stage, suggesting a key role in regulating host life activities and providing a theoretical basis for developing RNA-based pesticides to control ARD. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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18 pages, 2894 KiB

Open AccessArticle

Comparative Genomics and Pathogenicity Analysis of Three Fungal Isolates Causing Barnyard Grass Blast

by Na Zhang, Xinyang Li, Liangping Ming, Wenda Sun, Xiaofang Xie, Cailing Zhi, Xiaofan Zhou, Yanhua Wen, Zhibin Liang and Yizhen Deng

J. Fungi 2024, 10(12), 868; https://doi.org/10.3390/jof10120868 - 13 Dec 2024

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Abstract

Barnyard grass is one of the most serious rice weeds, often growing near paddy fields and therefore potentially serving as a bridging host for the rice blast fungus. In this study, we isolated three fungal strains from diseased barnyard grass leaves in a [...] Read more.

Barnyard grass is one of the most serious rice weeds, often growing near paddy fields and therefore potentially serving as a bridging host for the rice blast fungus. In this study, we isolated three fungal strains from diseased barnyard grass leaves in a rice field. Using a pathogenicity assay, we confirmed that they were capable of causing blast symptoms on barnyard grass and rice leaves to various extents. Based on morphology characterization and genome sequence analyses, we confirmed that these three strains were Epicoccum sorghinum (SCAU-1), Pyricularia grisea (SCAU-2), and Exserohilum rostratum (SCAU-6). The established Avirulence (Avr) genes Avr-Pia, Avr-Pita2, and ACE1 were detected by PCR amplification in SCAU-2, but not in SCAU-1 or SCAU-6. Furthermore, the whole-genome sequence analysis helped to reveal the genetic variations and potential virulence factors relating to the host specificity of these three fungal pathogens. Based on the evolutionary analysis of single-copy orthologous proteins, we found that the genes encoding glycoside hydrolases, carbohydrate esterases, oxidoreductase, and multidrug transporters in SCAU-1 and SCAU-6 were expanded, while expansion in SCAU-2 was mainly related to carbohydrate esterases. In summary, our study provides clues to understand the pathogenic mechanisms of fungal isolates from barnyard grass with the potential to cause rice blast. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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16 pages, 3793 KiB

Open AccessArticle

Comprehensive Genomic and Proteomic Analysis Identifies Effectors of Fusarium oxysporum f. sp. melongenae

by Jiayelu Wu, Pengfei Wang, Wuhong Wang, Haijiao Hu, Qingzhen Wei, Chonglai Bao and Yaqin Yan

J. Fungi 2024, 10(12), 828; https://doi.org/10.3390/jof10120828 - 28 Nov 2024

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Abstract

Fusarium wilt in eggplant caused by F. oxysporum f. sp. melongenae is a major devastating soil-borne disease on a worldwide scale. Effectors play important roles in the interactions in pathogen–plant interactions. Identifying effectors is essential for elucidating the pathogenic mechanisms of phytopathogenic fungi. [...] Read more.

Fusarium wilt in eggplant caused by F. oxysporum f. sp. melongenae is a major devastating soil-borne disease on a worldwide scale. Effectors play important roles in the interactions in pathogen–plant interactions. Identifying effectors is essential for elucidating the pathogenic mechanisms of phytopathogenic fungi. In this study, bioinformatic prediction approaches, including SignalP v5.0, TMHMM v2.0, WoLF PSORT, PredGPI, and EffectorP, were employed to screen for candidate secreted effector proteins (CSEPs) in F. oxysporum f. sp. melongenae. A total of 1019 proteins exhibiting characteristics typical of classical secretory proteins were identified, 301 of which demonstrated carbohydrate activity, and 194 CSEPs were identified. Furthermore, a total of 563 proteins from F. oxysporum f. sp. melongenae under induced conditions were identified using mass spectrometry-based label-free quantitative proteomics. These findings suggest a potential role of these CSEPs in the interaction between F. oxysporum f. sp. melongenae and eggplant, thereby contributing to a deeper understanding of the pathogenic mechanisms of F. oxysporum f. sp. melongenae and strategies for disease management. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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12 pages, 1984 KiB

Open AccessArticle

Chinese Populations of Magnaporthe oryzae Serving as a Source of Human-Mediated Gene Flow to Asian Countries: A Population Genomic Analysis

by Guohua Duan, Yuchan Liu, Cheng Zheng, Kaihui Yu, Jiahui Xie, Baohua Wang, Huakun Zheng, Wei Tang, Jiandong Bao, Zonghua Wang and Meilian Chen

J. Fungi 2024, 10(11), 739; https://doi.org/10.3390/jof10110739 - 25 Oct 2024

Viewed by 1502

Abstract

Magnaporthe oryzae, a filamentous heterothallic ascomycete fungus that serves as the causative agent of rice blast disease, is globally distributed in rice-growing regions. Populations shaped by environmental factors and human intervention play important roles in the formation of genetic structure. In this [...] Read more.

Magnaporthe oryzae, a filamentous heterothallic ascomycete fungus that serves as the causative agent of rice blast disease, is globally distributed in rice-growing regions. Populations shaped by environmental factors and human intervention play important roles in the formation of genetic structure. In this study, population structures and spatiotemporal dynamics were investigated based on large-scale whole genomic sequences of rice-infecting M. oryzae around the world. By analyzing these genetic structures, we identified divergent clades that crossed geographic boundaries. While we observed associations between the isolates and their geographic origins, we also found that there were frequent migration events occurring across Asia in main rice cultivation regions. Within Asia, China was the migration origin, facilitating gene flows to Japan and South Korea. Since the 1970s, the genetic diversity of M. oryzae populations in China has also shown a steadily increasing trend, continuing through to the 2020s. Additionally, our analysis of the evolutionary history of Asian M. oryzae populations provided insights into the population expansion that has taken place in recent decades. Overall, our findings indicate that human-mediated gene flows played a pivotal role in shaping the genetic structure of M. oryzae. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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12 pages, 5675 KiB

Open AccessArticle

Two Sugarcane Expansin Protein-Coding Genes Contribute to Stomatal Aperture Associated with Structural Resistance to Sugarcane Smut

by Zongling Liu, Zhuoxin Yu, Xiufang Li, Qin Cheng and Ru Li

J. Fungi 2024, 10(9), 631; https://doi.org/10.3390/jof10090631 - 3 Sep 2024

Viewed by 1298

Abstract

Sporisorium scitamineum is a biotrophic fungus responsible for inducing sugarcane smut disease that results in significant reductions in sugarcane yield. Resistance mechanisms against sugarcane smut can be categorized into structural, biochemical, and physiological resistance. However, structural resistance has been relatively understudied. This study [...] Read more.

Sporisorium scitamineum is a biotrophic fungus responsible for inducing sugarcane smut disease that results in significant reductions in sugarcane yield. Resistance mechanisms against sugarcane smut can be categorized into structural, biochemical, and physiological resistance. However, structural resistance has been relatively understudied. This study found that sugarcane variety ZZ9 displayed structural resistance compared to variety GT42 when subjected to different inoculation methods for assessing resistance to smut disease. Furthermore, the stomatal aperture and density of smut-susceptible varieties (ROC22 and GT42) were significantly higher than those of smut-resistant varieties (ZZ1, ZZ6, and ZZ9). Notably, S. scitamineum was found to be capable of entering sugarcane through the stomata on buds. According to the RNA sequencing of the buds of GT42 and ZZ9, seven Expansin protein-encoding genes were identified, of which six were significantly upregulated in GT42. The two genes c111037.graph_c0 and c113583.graph_c0, belonging to the α-Expansin and β-Expansin families, respectively, were functionally characterized, revealing their role in increasing the stomatal aperture. Therefore, these two sugarcane Expansin protein-coding genes contribute to the stomatal aperture, implying their potential roles in structural resistance to sugarcane smut. Our findings deepen the understanding of the role of the stomata in structural resistance to sugarcane smut and highlight their potential in sugarcane breeding for disease resistance. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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15 pages, 4794 KiB

Open AccessArticle

Complete Annotated Genome Assembly of Flax Pathogen Colletotrichum lini

by Elizaveta A. Sigova, Ekaterina M. Dvorianinova, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Daiana A. Zhernova, Antoniy M. Kaplun, Valeria A. Pavlova, Yakov V. Bodrov, Alexander A. Arkhipov, Elena V. Borkhert, Elena N. Pushkova, Nataliya V. Melnikova and Alexey A. Dmitriev

J. Fungi 2024, 10(9), 605; https://doi.org/10.3390/jof10090605 - 26 Aug 2024

Cited by 1 | Viewed by 1333

Abstract

Colletotrichum lini is a fungal pathogen of flax that can cause significant yield and quality losses. In this work, we obtained the first complete annotated genome assembly of the highly virulent C. lini strain #394-2. The nuclear genome consisted of ten core and [...] Read more.

Colletotrichum lini is a fungal pathogen of flax that can cause significant yield and quality losses. In this work, we obtained the first complete annotated genome assembly of the highly virulent C. lini strain #394-2. The nuclear genome consisted of ten core and two accessory chromosomes and had a length of 53.7 Mb. The mitochondrial genome was 39.1 kb. The assembly was obtained by the Canu–Racon ×2–Medaka–Polca algorithm using Oxford Nanopore Technologies and Illumina data. As a result of the annotation with the Illumina RNA-Seq data, 12,449 genes were identified. Potential signaling proteins were tested for effector functions and 550 effector proteins were predicted using EffectorP. The visualization of the effector protein localization revealed that the presence of effector proteins was associated with repeat-rich regions. A comparison of the genomic structure of C. lini with chromosome-level and complete assemblies of the genus Colletotrichum representatives revealed that the genomes of Colletotrichum species differed by the presence of chromosomal rearrangements. The obtained assembly expands the knowledge of the genomic structure of Colletotrichum species and provides the basis for further studies of C. lini, which will help to understand the virulence mechanisms and protect flax from anthracnose. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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Review

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25 pages, 1159 KiB

Open AccessReview

Emerging Roles of Exocyst Complex in Fungi: A Review

by Qussai Zuriegat, Yakubu Saddeeq Abubakar, Zonghua Wang, Meilian Chen and Jun Zhang

J. Fungi 2024, 10(9), 614; https://doi.org/10.3390/jof10090614 - 28 Aug 2024

Cited by 2 | Viewed by 1510

Abstract

The exocyst complex, an evolutionarily conserved octameric protein assembly, plays a central role in the targeted binding and fusion of vesicles at the plasma membrane. In fungal cells, this transport system is essential for polarized growth, morphogenesis, cell wall maintenance and virulence. Recent [...] Read more.

The exocyst complex, an evolutionarily conserved octameric protein assembly, plays a central role in the targeted binding and fusion of vesicles at the plasma membrane. In fungal cells, this transport system is essential for polarized growth, morphogenesis, cell wall maintenance and virulence. Recent advances have greatly improved our understanding of the role and regulation of the exocyst complex in fungi. This review synthesizes these developments and focuses on the intricate interplay between the exocyst complex, specific fungal cargos and regulatory proteins. Insights into thestructure of the exocyst and its functional dynamics have revealed new dimensions of its architecture and its interactions with the cellular environment. Furthermore, the regulation of exocyst activity involves complex signaling pathways and interactions with cytoskeletal elements that are crucial for its role in vesicle trafficking. By exploring these emerging themes, this review provides a comprehensive overview of the multifaceted functions of the exocyst complex in fungal biology. Understanding these mechanisms offers potential avenues for novel therapeutic strategies against fungal pathogens and insights into the general principles of vesicle trafficking in eukaryotic cells. The review therefore highlights the importance of the exocyst complex in maintaining cellular functions and its broader implications in fungal pathogenicity and cell biology. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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