Classification across the major fungal databases – the need for standardization

Le résumé fourni par la source

Online fungal databases are essential resources for nomenclature, classification, sequence identification, biodiversity assessment and applied mycology. However, because these databases are curated independently and updated at different times, inconsistencies in taxonomic placement can occur across platforms. In this study, we compared 10,693 genus-level records from the 2024 Outline of Fungi and fungus-like taxa with corresponding classifications in Species Fungorum, MycoBank, Fungal Names, GenBank and UNITE to evaluate the extent and nature of classification discrepancies among major fungal databases. Classifications were compared at the ranks of family, order, subclass, class, subphylum and phylum. Disagreements were detected at all examined ranks, with the highest number of conflicts occurring at the family level, followed by order, subclass, class, subphylum and phylum. Of the 10,693 genera included, 6,127 (57.29%) had differences between the 2024 Outline of Fungi and fungus-like taxa with corresponding classifications in Species Fungorum, MycoBank, Fungal Names, GenBank and UNITE. To provide biological context for these database-level patterns, selected case studies were examined from major fungal groups (in different ranks), including Agaricales, Diaporthales (Orders), Xylariomycetidae (Sub Class), Dothi¬deomycetes, Eurotiomycetes, Sordariomycetes (Classes), Basidiomycota (Phylum), lichenized fungi, plant pathogens, yeasts, and non-Dikarya (Sub Kingdom). These case studies illustrate how inconsistencies arise from rapid phylogenetic revision, unstable family boundaries, asynchronous database updates, incomplete adoption of recent classifications, inconsistent treatment of incertae sedis taxa, historical classification concepts, and cross-code homonyms. Particularly problematic were cases in which fungal generic names were linked to plant, algal and protist (Microsporidia and Rozellomycota) classifications in broader biological databases. Such inconsistencies have important consequences for fungal taxonomy, biodiversity inventories, ecological studies, sequence annotation, metabarcoding, plant pathology, medical mycology, biotechnology, and conservation research. The purpose of this paper is to show the inconsistencies across the main fungal databases in order to promote a move towards standardization and is not a criticism of any database, which requires huge resources to maintain. We, however, recommend improved synchronization among major fungal databases, the use of stable and kingdom-aware taxon identifiers, clearer treatment of homonyms and uncertain placements, complete hierarchical classifications, versioned updates, and links to supporting literature. This study highlights the need for a standardized, transparent and interoperable fungal classification framework to improve the reliability and reproducibility of fungal research.

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