Vol. 64 No. 3 (2025)
Articles

The most informative loci to identify trunk disease pathogens associated with grapevine and perennial fruit and nut crops

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  • David GRAMAJE,
  • Lizel MOSTERT,
  • Florent P. TROUILLAS,
  • Jose Ramon URBEZ TORRES,
  • Artur ALVES
David GRAMAJE
Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
Lizel MOSTERT
Department of Pant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
Florent P. TROUILLAS
Department of Plant Pathology, University of California, Davis and Kearney Agricultural Research and Extension Center, Parlier, CA, 93648, United States of America
Jose Ramon URBEZ TORRES
Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Box 5000. Summerland, BC V0H 1Z0, Canada
Artur ALVES
Departamento de Biologia, CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
DOI: https://doi.org/10.36253/phyto-16857

Published 2025-12-30

Keywords

  • Fungal Taxonomy,
  • multi-locus phylogeny,
  • molecular identification,
  • pathogen diagnosis

How to Cite

[1]
D. GRAMAJE, L. MOSTERT, F. P. TROUILLAS, J. R. URBEZ TORRES, and A. ALVES, “The most informative loci to identify trunk disease pathogens associated with grapevine and perennial fruit and nut crops”, Phytopathol. Mediterr., vol. 64, no. 3, pp. 631–636, Dec. 2025.

Copyright (c) 2025 David GRAMAJE, Lizel MOSTERT, Florent P. TROUILLAS, Jose Ramon URBEZ TORRES, Artur ALVES

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

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Abstract

Trunk disease (TD) fungi are taxonomically diverse, and accurate species delimitation relies on multilocus phylogenetic analyses. However, the loci commonly employed vary among fungal groups, leading to inconsistencies in species recognition. This paper provides a comparative overview of the most informative genetic loci for species identification within the main families associated with TDs, including Botryosphaeriaceae, Cytosporaceae, Diaporthaceae, Diatrypaceae, Phaeomoniellaceae, Togniniaceae, Nectriaceae (Ascomycota), and Hymenochaetales (Basidiomycota). The internal transcribed spacer region (ITS) remains the universal primary barcode, but its discriminatory power is often limited. The most informative loci [translation elongation factor 1-α (tef1), β-tubulin (tub2), actin (act1), calmodulin (cal), histone (his3), and the RNA polymerase II second largest subunit (rpb2)] are identified, and optimal locus combinations for each fungal group are identified. This synthesis will aid selection of the most appropriate loci for robust phylogenetic inference and accurate pathogen identification, thereby improving epidemiological and management studies of TDs.

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