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Genomics of Fungal Plant Pathogens, 2nd Edition
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Genomics of Fungal Plant Pathogens, 2nd 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 (29 February 2024) | Viewed by 17186

Special Issue Editors

Prof. Dr. Zonghua Wang

E-Mail Website
Guest Editor
1. Institute of Oceanography, Minjiang University, Fuzhou 350108, China
2. State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: molecular plant pathology; fungal genetic; molecular immunology
Special Issues, Collections and Topics in MDPI journals
Dr. Jun Huang

E-Mail Website
Co-Guest Editor
Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, USA
Interests: fungal molecular biology; fungal genetics; fungal bioinformatic

Special Issue Information

Dear Colleagues,

Fungi cause most of the severe plant diseases that endanger food safety worldwide. Resistance to fungal pathogens is a major target of breeders; however, the unexpected mutation of avirulence genes has caused a boom and burst cycle in resistance and resistance breakdown. Fungicide-based chemical control is still the most important method to control plant fungal diseases, but most fungicides induce fungi to develop fungicide resistance. Many scientists are working on these aspects to develop ecological control strategies for plant fungal diseases. Recent advances in sequencing technologies have led to remarkable progress in understanding plant–fungal interactions based on the dissection of fungal genomes. Many important plant pathogenic fungi have successfully been studied using the second- and third-generation sequencing approaches. Increasingly, functional genomics, proteomics, and metabolomics are being applied to study plant fungal pathogens. The development of advanced genomic tools and infrastructure is also making great progress. These increasing amounts of data will provide useful information to improve our understanding of the molecular mechanisms involved in host–pathogen interactions, in order to better understand fungal genome features, such as repetitive sequences, telomeres, conserved syntenic blocks, and the expansion of pathogenicity-related genes. The findings of these studies can be exploited to optimize beneficial interactions and to develop new plant-protection strategies.

This Special Issue is aimed at compiling research, reviews and opinion articles covering new scientific discoveries in plant–fungal genomics. Articles covering new insights in genomic sequencing, functional genomics, proteomics, metabolomics, molecular biology, ecology dissection, and the molecular mechanisms involved in plant–fungal interactions at the genome level are welcomed.

Prof. Dr. Zonghua Wang
Dr. Jun Huang
Guest Editors

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Published Papers (7 papers)

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Research

27 pages, 6496 KiB  
Article
Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics
by Perumal Nallathambi, Chandrasekaran Umamaheswari, Bhaskar Reddy, Balakrishnan Aarthy, Mohammed Javed, Priya Ravikumar, Santosh Watpade, Prem Lal Kashyap, Govindaraju Boopalakrishnan, Sudheer Kumar, Anju Sharma and Aundy Kumar
J. Fungi 2024, 10(4), 267; https://doi.org/10.3390/jof10040267 - 3 Apr 2024
Viewed by 3812
Abstract
A high-quality genome sequence from an Indian isolate of Blumeria graminis f. sp. tritici Wtn1, a persistent threat in wheat farming, was obtained using a hybrid method. The assembly of over 9.24 million DNA-sequence reads resulted in 93 contigs, totaling a 140.61 Mb [...] Read more.
A high-quality genome sequence from an Indian isolate of Blumeria graminis f. sp. tritici Wtn1, a persistent threat in wheat farming, was obtained using a hybrid method. The assembly of over 9.24 million DNA-sequence reads resulted in 93 contigs, totaling a 140.61 Mb genome size, potentially encoding 8480 genes. Notably, more than 73.80% of the genome, spanning approximately 102.14 Mb, comprises retro-elements, LTR elements, and P elements, influencing evolution and adaptation significantly. The phylogenomic analysis placed B. graminis f. sp. tritici Wtn1 in a distinct monocot-infecting clade. A total of 583 tRNA anticodon sequences were identified from the whole genome of the native virulent strain B. graminis f. sp. tritici, which comprises distinct genome features with high counts of tRNA anticodons for leucine (70), cysteine (61), alanine (58), and arginine (45), with only two stop codons (Opal and Ochre) present and the absence of the Amber stop codon. Comparative InterProScan analysis unveiled “shared and unique” proteins in B. graminis f. sp. tritici Wtn1. Identified were 7707 protein-encoding genes, annotated to different categories such as 805 effectors, 156 CAZymes, 6102 orthologous proteins, and 3180 distinct protein families (PFAMs). Among the effectors, genes like Avra10, Avrk1, Bcg-7, BEC1005, CSEP0105, CSEP0162, BEC1016, BEC1040, and HopI1 closely linked to pathogenesis and virulence were recognized. Transcriptome analysis highlighted abundant proteins associated with RNA processing and modification, post-translational modification, protein turnover, chaperones, and signal transduction. Examining the Environmental Information Processing Pathways in B. graminis f. sp. tritici Wtn1 revealed 393 genes across 33 signal transduction pathways. The key pathways included yeast MAPK signaling (53 genes), mTOR signaling (38 genes), PI3K-Akt signaling (23 genes), and AMPK signaling (21 genes). Additionally, pathways like FoxO, Phosphatidylinositol, the two-component system, and Ras signaling showed significant gene representation, each with 15–16 genes, key SNPs, and Indels in specific chromosomes highlighting their relevance to environmental responses and pathotype evolution. The SNP and InDel analysis resulted in about 3.56 million variants, including 3.45 million SNPs, 5050 insertions, and 5651 deletions within the whole genome of B. graminis f. sp. tritici Wtn1. These comprehensive genome and transcriptome datasets serve as crucial resources for understanding the pathogenicity, virulence effectors, retro-elements, and evolutionary origins of B. graminis f. sp. tritici Wtn1, aiding in developing robust strategies for the effective management of wheat powdery mildew. Full article
(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 2nd Edition)
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14 pages, 11765 KiB  
Article
The Sclerotinia sclerotiorum ADP-Ribosylation Factor 6 Plays an Essential Role in Abiotic Stress Response and Fungal Virulence to Host Plants
by Kunmei Wang, Siyi Wang, Ting Wang, Qi Xia and Shitou Xia
J. Fungi 2024, 10(1), 12; https://doi.org/10.3390/jof10010012 - 25 Dec 2023
Cited by 1 | Viewed by 1374
Abstract
The ADP-ribosylation factor 6 (Arf6), as the only member of the Arf family III protein, has been extensively studied for its diverse biological functions in animals. Previously, the Arf6 protein in Magnaporthe oryzae was found to be crucial for endocytosis and polarity establishment [...] Read more.
The ADP-ribosylation factor 6 (Arf6), as the only member of the Arf family III protein, has been extensively studied for its diverse biological functions in animals. Previously, the Arf6 protein in Magnaporthe oryzae was found to be crucial for endocytosis and polarity establishment during asexual development. However, its role remains unclear in S. sclerotiorum. Here, we identified and characterized SsArf6 in S. sclerotiorum using a reverse genetic approach. Deletion of SsArf6 impaired hyphal growth and development and produced more branches. Interestingly, knockout of SsArf6 resulted in an augmented tolerance of S. sclerotiorum towards oxidative stress, and increased its sensitivity towards osmotic stress, indicative of the different roles of SsArf6 in various stress responses. Simultaneously, SsArf6 deletion led to an elevation in melanin accumulation. Moreover, the appressorium formation was severely impaired, and fungal virulence to host plants was significantly reduced. Overall, our findings demonstrate the essential role of SsArf6 in hyphal development, stress responses, appressorium formation, and fungal virulence to host plants. Full article
(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 2nd Edition)
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14 pages, 9710 KiB  
Article
Functional Analysis of a Salicylate Hydroxylase in Sclerotinia sclerotiorum
by Shengfei He, Kun Huang, Baoge Li, Guodong Lu and Airong Wang
J. Fungi 2023, 9(12), 1169; https://doi.org/10.3390/jof9121169 - 5 Dec 2023
Cited by 1 | Viewed by 1628
Abstract
Salicylic acid plays a crucial role during plant defense to Sclerotinia sclerotiorum. Some bacteria and a few fungi can produce salicylate hydroxylase to degrade SA to suppress plant defense and increase their virulence. But there has been no single salicylate hydroxylase in [...] Read more.
Salicylic acid plays a crucial role during plant defense to Sclerotinia sclerotiorum. Some bacteria and a few fungi can produce salicylate hydroxylase to degrade SA to suppress plant defense and increase their virulence. But there has been no single salicylate hydroxylase in Sclerotinia sclerotiorum identified until now. In this study, we found that SS1G_02963 (SsShy1), among several predicted salicylate hydroxylases in S. sclerotiorum, was induced approximately 17.6-fold during infection, suggesting its potential role in virulence. SsShy1 could catalyze the conversion of SA to catechol when heterologous expression in E. coli. Moreover, overexpression of SsShy1 in Arabidopsis thaliana decreased the SA concentration and the resistance to S. sclerotiorum, confirming that SsShy1 is a salicylate hydroxylase. Deletion mutants of SsShy1 (∆Ssshy1) showed slower growth, less sclerotia production, more sensitivity to exogenous SA, and lower virulence to Brassica napus. The complemented strain with a functional SsShy1 gene recovered the wild-type phenotype. These results indicate that SsShy1 plays an important role in growth and sclerotia production of S. sclerotiorum, as well as the ability to metabolize SA affects the virulence of S. sclerotiorum. Full article
(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 2nd Edition)
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18 pages, 1529 KiB  
Article
Dose-Dependent Genetic Resistance to Azole Fungicides Found in the Apple Scab Pathogen
by Thomas Heaven, Andrew D. Armitage, Xiangming Xu, Matthew R. Goddard and Helen M. Cockerton
J. Fungi 2023, 9(12), 1136; https://doi.org/10.3390/jof9121136 - 24 Nov 2023
Viewed by 1744
Abstract
The evolution of azole resistance in fungal pathogens presents a major challenge in both crop production and human health. Apple orchards across the world are faced with the emergence of azole fungicide resistance in the apple scab pathogen Venturia inaequalis. Target site [...] Read more.
The evolution of azole resistance in fungal pathogens presents a major challenge in both crop production and human health. Apple orchards across the world are faced with the emergence of azole fungicide resistance in the apple scab pathogen Venturia inaequalis. Target site point mutations observed in this fungus to date cannot fully explain the reduction in sensitivity to azole fungicides. Here, polygenic resistance to tebuconazole was studied across a population of V. inaequalis. Genotyping by sequencing allowed Quantitative Trait Loci (QTLs) mapping to identify the genetic components controlling this fungicide resistance. Dose-dependent genetic resistance was identified, with distinct genetic components contributing to fungicide resistance at different exposure levels. A QTL within linkage group seven explained 65% of the variation in the effective dose required to reduce growth by 50% (ED50). This locus was also involved in resistance at lower fungicide doses (ED10). A second QTL in linkage group one was associated with dose-dependent resistance, explaining 34% of variation at low fungicide doses (ED10), but did not contribute to resistance at higher doses (ED50 and ED90). Within QTL regions, non-synonymous mutations were observed in several ATP-Binding Cassette and Major Facilitator SuperFamily transporter genes. These findings provide insight into the mechanisms of fungicide resistance that have evolved in horticultural pathogens. Identification of resistance gene candidates supports the development of molecular diagnostics to inform management practices. Full article
(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 2nd Edition)
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21 pages, 17081 KiB  
Article
Genomic and Transcriptomic Survey Provides Insights into Molecular Basis of Pathogenicity of the Sunflower Pathogen Phoma macdonaldii
by Xuejing Chen, Xiaoran Hao, Oren Akhberdi and Xudong Zhu
J. Fungi 2023, 9(5), 520; https://doi.org/10.3390/jof9050520 - 27 Apr 2023
Cited by 4 | Viewed by 1947
Abstract
Phoma macdonaldii (teleomorph Leptosphaeria lindquistii) is the causal agent of sunflower (Helianthus annuus L.) black stem. In order to investigate the molecular basis for the pathogenicity of P. ormacdonaldii, genomic and transcriptomic analyses were performed. The genome size was 38.24 [...] Read more.
Phoma macdonaldii (teleomorph Leptosphaeria lindquistii) is the causal agent of sunflower (Helianthus annuus L.) black stem. In order to investigate the molecular basis for the pathogenicity of P. ormacdonaldii, genomic and transcriptomic analyses were performed. The genome size was 38.24 Mb and assembled into 27 contigs with 11,094 putative predicted genes. These include 1133 genes for CAZymes specific for plant polysaccharide degradation, 2356 for the interaction between the pathogen and host, 2167 for virulence factors, and 37 secondary metabolites gene clusters. RNA-seq analysis was conducted at the early and late stages of the fungal spot formation in infected sunflower tissues. A total of 2506, 3035, and 2660 differentially expressed genes (DEGs) between CT and each treatment group (LEAF-2d, LEAF-6d, and STEM) were retrieved, respectively. The most significant pathways of DEGs from these diseased sunflower tissues were the metabolic pathways and biosynthesis of secondary metabolites. Overall, 371 up-regulated DEGs were shared among LEAF-2d, LEAF-6d, and STEM, including 82 mapped to DFVF, 63 mapped to PHI-base, 69 annotated as CAZymes, 33 annotated as transporters, 91 annotated as secretory proteins, and a carbon skeleton biosynthetic gene. The most important DEGs were further confirmed by RT-qPCR. This is the first report on the genome-scale assembly and annotation for P. macdonaldii. Our data provide a framework for further revealing the underlying mechanism of the pathogenesis of P. macdonaldii, and also suggest the potential targets for the diseases caused by this fungal pathogen. Full article
(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 2nd Edition)
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23 pages, 2525 KiB  
Article
Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex
by Houlin Yu, He Yang, Sajeet Haridas, Richard D. Hayes, Hunter Lynch, Sawyer Andersen, Madison Newman, Gengtan Li, Domingo Martínez-Soto, Shira Milo-Cochavi, Dilay Hazal Ayhan, Yong Zhang, Igor V. Grigoriev and Li-Jun Ma
J. Fungi 2023, 9(3), 359; https://doi.org/10.3390/jof9030359 - 15 Mar 2023
Cited by 3 | Viewed by 3019
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. [...] Read more.
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens. Full article
(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 2nd Edition)
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18 pages, 2178 KiB  
Article
Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data
by Elizaveta A. Sigova, Elena N. Pushkova, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Alexander A. Zhuchenko, Roman O. Novakovskiy, Daiana A. Zhernova, Liubov V. Povkhova, Anastasia A. Turba, Elena V. Borkhert, Nataliya V. Melnikova, Alexey A. Dmitriev and Ekaterina M. Dvorianinova
J. Fungi 2023, 9(3), 301; https://doi.org/10.3390/jof9030301 - 26 Feb 2023
Cited by 4 | Viewed by 2741
Abstract
Flax (Linum usitatissimum L.) is attacked by numerous devastating fungal pathogens, including Colletotrichum lini, Aureobasidium pullulans, and Fusarium verticillioides (Fusarium moniliforme). The effective control of flax diseases follows the paradigm of extensive molecular research on pathogenicity. However, such [...] Read more.
Flax (Linum usitatissimum L.) is attacked by numerous devastating fungal pathogens, including Colletotrichum lini, Aureobasidium pullulans, and Fusarium verticillioides (Fusarium moniliforme). The effective control of flax diseases follows the paradigm of extensive molecular research on pathogenicity. However, such studies require quality genome sequences of the studied organisms. This article reports on the approaches to assembling a high-quality fungal genome from the Oxford Nanopore Technologies data. We sequenced the genomes of C. lini, A. pullulans, and F. verticillioides (F. moniliforme) and received different volumes of sequencing data: 1.7 Gb, 3.9 Gb, and 11.1 Gb, respectively. To obtain the optimal genome sequences, we studied the effect of input data quality and genome coverage on assembly statistics and tested the performance of different assembling and polishing software. For C. lini, the most contiguous and complete assembly was obtained by the Flye assembler and the Homopolish polisher. The genome coverage had more effect than data quality on assembly statistics, likely due to the relatively low amount of sequencing data obtained for C. lini. The final assembly was 53.4 Mb long and 96.4% complete (according to the glomerellales_odb10 BUSCO dataset), consisted of 42 contigs, and had an N50 of 4.4 Mb. For A. pullulans and F. verticillioides (F. moniliforme), the best assemblies were produced by Canu–Medaka and Canu–Homopolish, respectively. The final assembly of A. pullulans had a length of 29.5 Mb, 99.4% completeness (dothideomycetes_odb10), an N50 of 2.4 Mb and consisted of 32 contigs. F. verticillioides (F. moniliforme) assembly was 44.1 Mb long, 97.8% complete (hypocreales_odb10), consisted of 54 contigs, and had an N50 of 4.4 Mb. The obtained results can serve as a guideline for assembling a de novo genome of a fungus. In addition, our data can be used in genomic studies of fungal pathogens or plant–pathogen interactions and assist in the management of flax diseases. Full article
(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 2nd Edition)
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