Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine 2.0

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 (25 March 2023) | Viewed by 2142

Special Issue Editors

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Guest Editor
Institute of Grapevine and Wine Sciences (ICVV), La Rioja, Spain
Interests: plant pathology; phytopathology; fungal disease; vitis vinifera; trunk disease; molecular diagnosis; fungal taxonomy; disease management; fungal microbiome
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Guest Editor
Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, 69144 Lednice, Czech Republic
Interests: high-throughput sequencing; bioinformatics; plant pathology; metagenomics; small RNA; grapevine trunk pathogens
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Grapevine trunk diseases (GTDs) have become a major concern worldwide, causing significant economic impacts due to reduced production and vineyard longevity. These diseases are caused by a wide range of fungal pathogens producing a range of symptoms, including leaf and shoot distortion and discoloration, external wood cankers and dieback, internal wood necrosis and staining, poor growth, mortality of roots, and sudden vine collapse. The prevalence of GTDs has significantly increased with changes in production practices, the loss of effective chemicals, predominance of susceptible cultivars, and ageing of vineyards. Successful disease management requires a holistic approach from the nursery to the vineyard.

Over the last several decades, the study of plant–pathogen interactions was boosted by the advent of new technologies and the application of multiple omics platforms. Omics technologies reflect the dynamic concept of biological processes and provide a contemporary approach to mycology research for fungal pathogen management by identifying whole genomes (genomics); epigenetic mechanisms (epigenomics); transcriptomes (transcriptomics), proteomes (proteomics), and metabolomes (metabolomics); bacterial and fungal communities, protozoa, viruses, and viroids (metagenomics); the total elemental composition of organisms (ionomics); the structure and function of the complete set of lipids (lipidomics); and phenotypes (phenomics).

The aim of this Special Issue is to cover multiple aspects of grapevine fungal trunk pathogen interactions, with an emphasis on the application of individual- and multi-omics-based technologies to propose novel or improve the current management strategies.

Dr. David Gramaje
Dr. Ales Eichmeier
Guest Editors

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  • NGS, HTS
  • bioinformatics
  • multi-omics
  • small molecules
  • grapevine trunk diseases
  • Vitis vinifera
  • multidisciplinary research

Published Papers (1 paper)

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26 pages, 8646 KiB  
Wood Degradation by Fomitiporia mediterranea M. Fischer: Exploring Fungal Adaptation Using Metabolomic Networking
by Marion Schilling, Marceau Levasseur, Muriel Barbier, Lydie Oliveira-Correia, Céline Henry, David Touboul, Sibylle Farine, Christophe Bertsch and Eric Gelhaye
J. Fungi 2023, 9(5), 536; - 30 Apr 2023
Cited by 2 | Viewed by 1813
Fomitiporia mediterranea M. Fischer (Fmed) is a white-rot wood-decaying fungus associated with one of the most important and challenging diseases in vineyards: Esca. To relieve microbial degradation, woody plants, including Vitis vinifera, use structural and chemical weapons. Lignin is the most recalcitrant [...] Read more.
Fomitiporia mediterranea M. Fischer (Fmed) is a white-rot wood-decaying fungus associated with one of the most important and challenging diseases in vineyards: Esca. To relieve microbial degradation, woody plants, including Vitis vinifera, use structural and chemical weapons. Lignin is the most recalcitrant of the wood cell wall structural compounds and contributes to wood durability. Extractives are constitutive or de novo synthesized specialized metabolites that are not covalently bound to wood cell walls and are often associated with antimicrobial properties. Fmed is able to mineralize lignin and detoxify toxic wood extractives, thanks to enzymes such as laccases and peroxidases. Grapevine wood’s chemical composition could be involved in Fmed’s adaptation to its substrate. This study aimed at deciphering if Fmed uses specific mechanisms to degrade grapevine wood structure and extractives. Three different wood species, grapevine, beech, and oak. were exposed to fungal degradation by two Fmed strains. The well-studied white-rot fungus Trametes versicolor (Tver) was used as a comparison model. A simultaneous degradation pattern was shown for Fmed in the three degraded wood species. Wood mass loss after 7 months for the two fungal species was the highest with low-density oak wood. For the latter wood species, radical differences in initial wood density were observed. No differences between grapevine or beech wood degradation rates were observed after degradation by Fmed or by Tver. Contrary to the Tver secretome, one manganese peroxidase isoform (MnP2l, jgi protein ID 145801) was the most abundant in the Fmed secretome on grapevine wood only. Non-targeted metabolomic analysis was conducted on wood and mycelium samples, using metabolomic networking and public databases (GNPS, MS-DIAL) for metabolite annotations. Chemical differences between non-degraded and degraded woods, and between mycelia grown on different wood species, are discussed. This study highlights Fmed physiological, proteomic and metabolomic traits during wood degradation and thus contributes to a better understanding of its wood degradation mechanisms. Full article
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