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

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.