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Molecular and Genetic Diversity in Plant-Pathogenic Fungi
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Molecular and Genetic Diversity in Plant-Pathogenic Fungi

A special issue of Journal of Fungi (ISSN 2309-608X).

Deadline for manuscript submissions: closed (1 April 2023) | Viewed by 13615

Special Issue Editors

Dr. Matias Pasquali

E-Mail Website
Guest Editor
Department of Food, Environmental and Nutritional Sciences, University of Milan, Milano MI, Italy
Interests: fungal diversity; functional genomics; plant pathogens; mycotoxins
Dr. Marco Saracchi

E-Mail Website
Guest Editor
Department of Food, Environmental and Nutritional Sciences, University of Milan, Milano MI, Italy
Interests: mycology; plant pathogens; fungal diversity; biocontrol; actinomycetes
Dr. Andrea Kunova

E-Mail Website
Guest Editor
Department of Food, Environmental and Nutritional Sciences, University of Milan, Milano MI, Italy
Interests: novel molecules for fungal disease management; biocontrol; molecular bases of fungicide resistance

Special Issue Information

Dear Colleagues,

Plant diseases caused by fungi are a significant cause of losses for agricultural production, forests’ wellbeing, and urban environments. Every control strategy requires deep knowledge of the diversity within the target species. Molecular and genomic tools are essential for the species definition and grouping of pathogens. This Special Issue welcomes manuscripts that employ state-of-the-art approaches to describe the fungal diversity of fungal plant pathogens. Population studies among fungal populations of pathogens are the core of this Special Issue.

Both large-scale studies on known species as well as novel population studies on recently emerged plant pathogens are welcome. For this Special Issue, we invite reviews and original research papers on the application of molecular and genomics tools to the fungal diversity of plant pathogens. Systematic and molecular phylogeny works on plant pathogens are welcome.

Dr. Matias Pasquali
Dr. Marco Saracchi
Dr. Andrea Kunova
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. 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

  • plant-pathogen diversity
  • genomics
  • plant-pathogen systematics
  • agricultural fungal pathogens
  • forest fungal pathogens

Published Papers (6 papers)

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Research

16 pages, 4656 KiB  
Article
Inventory of the Secondary Metabolite Biosynthetic Potential of Members within the Terminal Clade of the Fusarium solani Species Complex
by Ambika Pokhrel and Jeffrey J. Coleman
J. Fungi 2023, 9(8), 799; https://doi.org/10.3390/jof9080799 - 28 Jul 2023
Viewed by 969
Abstract
The Fusarium solani species complex (FSSC) constitutes at least 77 phylogenetically distinct species including several agriculturally important and clinically relevant opportunistic pathogens. As with other Fusaria, they have been well documented to produce many secondary metabolites—compounds that are not required for the fungus [...] Read more.
The Fusarium solani species complex (FSSC) constitutes at least 77 phylogenetically distinct species including several agriculturally important and clinically relevant opportunistic pathogens. As with other Fusaria, they have been well documented to produce many secondary metabolites—compounds that are not required for the fungus to grow or develop but may be beneficial to the organism. An analysis of ten genomes from fungi within the terminal clade (clade 3) of the FSSC revealed each genome encoded 35 (F. cucurbitcola) to 48 (F. tenucristatum) secondary metabolite biosynthetic gene clusters (BGCs). A total of seventy-four different BGCs were identified from the ten FSSC genomes including seven polyketide synthases (PKS), thirteen nonribosomal peptide synthetases (NRPS), two terpene synthase BGCs, and a single dimethylallytryptophan synthase (DMATS) BGC conserved in all the genomes. Some of the clusters that were shared included those responsible for producing naphthoquinones such as fusarubins, a red pigmented compound, squalestatin, and the siderophores malonichrome, ferricrocin, and triacetylfusarinine. Eight novel NRPS and five novel PKS BGCs were identified, while BGCs predicted to produce radicicol, gibberellin, and fusaoctaxin were identified, which have not previously described in members of the FSSC. The diversity of the secondary metabolite repertoire of the FSSC may contribute to the expansive host range of these fungi and their ability to colonize broad habitats. Full article
(This article belongs to the Special Issue Molecular and Genetic Diversity in Plant-Pathogenic Fungi)
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12 pages, 1005 KiB  
Article
High Genetic Diversity and Structure of Colletotrichum gloeosporioides s.l. in the Archipelago of Lesser Antilles
by Pauline Dentika, Jean-Marc Blazy, Angela Alleyne, Dalila Petro, Anderson Eversley and Laurent Penet
J. Fungi 2023, 9(6), 619; https://doi.org/10.3390/jof9060619 - 27 May 2023
Viewed by 1113
Abstract
Colletotrichum gloeosporioides is a species complex of agricultural importance as it causes anthracnose disease on many crop species worldwide, and strong impact regionally on Water Yam (Dioscorea alata) in the Caribbean. In this study, we conducted a genetic analysis of the [...] Read more.
Colletotrichum gloeosporioides is a species complex of agricultural importance as it causes anthracnose disease on many crop species worldwide, and strong impact regionally on Water Yam (Dioscorea alata) in the Caribbean. In this study, we conducted a genetic analysis of the fungi complex in three islands of the Lesser Antilles—Guadeloupe (Basse Terre, Grande Terre and Marie Galante), Martinique and Barbados. We specifically sampled yam fields and assessed the genetic diversity of strains with four microsatellite markers. We found a very high genetic diversity of all strains on each island, and intermediate to strong levels of genetic structure between islands. Migration rates were quite diverse either within (local dispersal) or between islands (long-distance dispersal), suggesting important roles of vegetation and climate as local barriers, and winds as an important factor in long-distance migration. Three distinct genetic clusters highlighted different species entities, though there was also evidence of frequent intermediates between two clusters, suggesting recurrent recombination between putative species. Together, these results demonstrated asymmetries in gene flow both between islands and clusters, and suggested the need for new approaches to anthracnose disease risk control at a regional level. Full article
(This article belongs to the Special Issue Molecular and Genetic Diversity in Plant-Pathogenic Fungi)
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27 pages, 7203 KiB  
Article
A Metagenomic Survey of Wood Decay Fungi in the Urban Trees of Singapore
by Yan Hong, Jhing Yein Tan, Huiyu Xue, Mei Lun Chow, Mohamed Ali, Arthur Ng, Abigail Leong, Jeb Yeo, Shao Ming Koh, Megan Shi Ying Tang, Yan Yi Lee, Amy Mei Fun Choong, Serena Mei Lyn Lee, Riccardo Delli Ponti, Perry M. Chan, Daryl Lee, Jia Yih Wong, Marek Mutwil and Yok King Fong
J. Fungi 2023, 9(4), 460; https://doi.org/10.3390/jof9040460 - 10 Apr 2023
Cited by 3 | Viewed by 4014
Abstract
Mature tropical urban trees are susceptible to root and trunk rot caused by pathogenic fungi. A metagenomic survey of such fungi was carried out on 210 soil and tissue samples collected from 134 trees of 14 common species in Singapore. Furthermore, 121 fruiting [...] Read more.
Mature tropical urban trees are susceptible to root and trunk rot caused by pathogenic fungi. A metagenomic survey of such fungi was carried out on 210 soil and tissue samples collected from 134 trees of 14 common species in Singapore. Furthermore, 121 fruiting bodies were collected and barcoded. Out of the 22,067 OTUs (operational taxonomic units) identified, 10,646 OTUs had annotation information, and most were either ascomycetes (63.4%) or basidiomycetes (22.5%). Based on their detection in the diseased tissues and surrounding soils and/or the presence of fruiting bodies, fourteen basidiomycetes (nine Polyporales, four Hymenochaetales, one Boletales) and three ascomycetes (three species of Scytalidium) were strongly associated with the diseased trees. Fulvifomes siamensis affected the largest number of tree species surveyed. The association of three fungi was further supported by in vitro wood decay studies. Genetic heterogeneity was common in the diseased tissues and fruiting bodies (Ganoderma species especially). This survey identified the common pathogenic fungi of tropical urban trees and laid the foundation for early diagnosis and targeted mitigation efforts. It also illustrated the complexity of fungal ecology and pathogenicity. Full article
(This article belongs to the Special Issue Molecular and Genetic Diversity in Plant-Pathogenic Fungi)
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14 pages, 2704 KiB  
Article
Silencing of the Transmembrane Transporter (swnT) Gene of the Fungus Slafractonia leguminicola Results in a Reduction of Mycotoxin Transport
by Sumanjari Das, Dale R. Gardner, Marwa Neyaz, Allen B. Charleston III, Daniel Cook and Rebecca Creamer
J. Fungi 2023, 9(3), 370; https://doi.org/10.3390/jof9030370 - 18 Mar 2023
Cited by 2 | Viewed by 1363
Abstract
Slafractonia leguminicola infects red clover and other legumes, causing black patch disease. This pathogenic fungus also produces two mycotoxins, slaframine and swainsonine, that are toxic to livestock grazing on clover hay or pasture infested with S. leguminicola. Swainsonine toxicosis causes locoism, while [...] Read more.
Slafractonia leguminicola infects red clover and other legumes, causing black patch disease. This pathogenic fungus also produces two mycotoxins, slaframine and swainsonine, that are toxic to livestock grazing on clover hay or pasture infested with S. leguminicola. Swainsonine toxicosis causes locoism, while slaframine causes slobbers syndrome. The mechanism of toxin secretion by S. leguminicola is poorly understood. The aim of this research was to investigate the role of a putative transmembrane transporter, SwnT, in mycotoxin transport. The swnT gene was silenced by RNA interference using the silencing vector Psilent1, which included inverted repeat transgenes of swnT. This resulted in a significant reduction of swnT transcript levels compared with the controls. Silencing caused a decline in the active efflux of toxins from the mycelia to the media, as shown by LC–MS analysis. Transformants in which swnT was silenced showed higher concentrations of both toxins in the mycelia compared with the concentrations in the media. These transformants exhibited a visibly distinct phenotype with much thicker and shorter mycelia than in the wild type. These transformants were also unable to infect detached clover leaves, unlike the controls, suggesting that SwnT function may play an important role in pathogenesis in addition to mycotoxin transport. This research demonstrates the importance of this transporter to the secretion of mycotoxins for this phytopathogenic fungus. Full article
(This article belongs to the Special Issue Molecular and Genetic Diversity in Plant-Pathogenic Fungi)
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13 pages, 2193 KiB  
Article
Development of Diagnostic Markers and Applied for Genetic Diversity Study and Population Structure of Bipolaris sorokiniana Associated with Leaf Blight Complex of Wheat
by Abhijeet Shankar Kashyap, Nazia Manzar, Avantika Maurya, Deendayal Das Mishra, Ravinder Pal Singh and Pawan Kumar Sharma
J. Fungi 2023, 9(2), 153; https://doi.org/10.3390/jof9020153 - 23 Jan 2023
Cited by 7 | Viewed by 1613
Abstract
Bipolaris sorokiniana, a key pathogenic fungus in the wheat leaf blight complex, was the subject of research that resulted in the development of fifty-five polymorphic microsatellite markers. These markers were then used to examine genetic diversity and population structure in Indian geographical [...] Read more.
Bipolaris sorokiniana, a key pathogenic fungus in the wheat leaf blight complex, was the subject of research that resulted in the development of fifty-five polymorphic microsatellite markers. These markers were then used to examine genetic diversity and population structure in Indian geographical regions. The simple sequence repeat (SSR) like trinucleotides, dinucleotides, and tetranucleotides accounted for 43.37% (1256), 23.86% (691), and 16.54% (479) of the 2896 microsatellite repeats, respectively. There were 109 alleles produced by these loci overall, averaging 2.36 alleles per microsatellite marker. The average polymorphism information content value was 0.3451, with values ranging from 0.1319 to 0.5932. The loci’s Shannon diversity varied from 0.2712 to 1.2415. These 36 isolates were divided into two main groups using population structure analysis and unweighted neighbour joining. The groupings were not based on where the isolates came from geographically. Only 7% of the overall variation was found to be between populations, according to an analysis of molecular variance. The high amount of gene flow estimate (NM = 3.261 per generation) among populations demonstrated low genetic differentiation in the entire populations (FST = 0.071). The findings indicate that genetic diversity is often minimal. In order to examine the genetic diversity and population structure of the B. sorokiniana populations, the recently produced microsatellite markers will be helpful. This study’s findings may serve as a foundation for developing improved management plans for the leaf blight complex and spot blotch of wheat diseases in India. Full article
(This article belongs to the Special Issue Molecular and Genetic Diversity in Plant-Pathogenic Fungi)
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12 pages, 2373 KiB  
Article
Alternaria alternata, the Causal Agent of a New Needle Blight Disease on Pinus bungeana
by Mao-Jiao Zhang, Xiang-Rong Zheng, Huan Li and Feng-Mao Chen
J. Fungi 2023, 9(1), 71; https://doi.org/10.3390/jof9010071 - 03 Jan 2023
Cited by 7 | Viewed by 3788
Abstract
Pinus bungeana, an endangered and native coniferous tree species in China, has considerable timber and horticulture value. However, little is known about needle diseases in P. bungeana. A needle blight of P. bungeana has been observed in Hebei Province, China. P. [...] Read more.
Pinus bungeana, an endangered and native coniferous tree species in China, has considerable timber and horticulture value. However, little is known about needle diseases in P. bungeana. A needle blight of P. bungeana has been observed in Hebei Province, China. P. bungeana inoculated with mycelial plugs of fungal isolates presented symptoms similar to those observed under field conditions. Ten virulent fungal isolates were identified as a small-spored Alternaria species based on morphological observations. Maximum likelihood and Bayesian phylogenetic analyses carried out with multilocus sequence typing of eight regions (SSU, LSU, ITS, gapdh, tef1, Alt a 1, endoPG, OPA10-2) assigned the pathogen to Alternaria alternata. This is the first report of A. alternata causing needle blight on P. bungeana in China. Full article
(This article belongs to the Special Issue Molecular and Genetic Diversity in Plant-Pathogenic Fungi)
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