Taxonomy of the Phylum Basidiomycota: A Critical Narrative Review of Molecular Phylogenetic Classification, Persistent Nodes of Uncertainty and Nomenclatural Change
K. Premalatha *
Centre of Excellence on Watershed Management, University of Agricultural Sciences, GKVK, Bangalore-5600065, India.
H. L. Soundarya
Centre of Excellence on Watershed Management, University of Agricultural Sciences, GKVK, Bangalore-5600065, India.
Keerthi Sharma
University of Agricultural Sciences, GKVK, Bangalore-5600065, India.
*Author to whom correspondence should be addressed.
Abstract
Background: Basidiomycota is the second-largest phylum of the kingdom Fungi and encompasses mushroom-forming fungi, jelly fungi, rust and smut pathogens, and numerous basidiomycetous yeasts, underpinning processes ranging from lignocellulose decomposition and ectomycorrhizal symbiosis to major diseases of cereal and other crops. Its higher-level classification has been substantially reorganised since the introduction of ribosomal DNA sequencing and multigene phylogenetics, yet several deep nodes and boundary questions remain contested.
Purpose and Scope: This critical narrative review synthesises molecular phylogenetic and phylogenomic evidence bearing on the classification of Basidiomycota, from the establishment of the three principal molecular subphyla through to the most recent kingdom-wide taxonomic outlines, with attention to methodological quality, convergent and conflicting findings, and unresolved taxonomic problems.
Approach: Evidence was drawn from peer-reviewed systematic, phylogenomic and nomenclatural studies identified through structured searches of major bibliographic and taxonomic sources, appraised for taxon sampling, locus and data type, analytical framework and congruence among independent datasets, and synthesised thematically rather than as a study-by-study catalogue.
Principal Themes: The review traces the transition from morphology-based classification to ribosomal, multilocus and, subsequently, genome-scale phylogenomic classification; examines the internal architecture of Agaricomycotina, Pucciniomycotina, Ustilaginomycotina and the more recently recognised Wallemiomycotina; addresses the contested phylum-level status of Entorrhizomycota; and considers species-level delimitation, DNA barcoding, cryptic diversity and the 2011 abandonment of dual nomenclature for pleomorphic fungi. Case studies of rust fungi, smut fungi and agaricoid clades illustrate how host-driven diversification, genomic sampling and convergent morphological evolution continue to reshape family- and order-level classification.
Unresolved Questions: Substantial disagreement persists over deep divergence times, the placement of several depauperate or long-branched lineages, the exact phylogenetic position of Entorrhizomycota relative to Basidiomycota, and the adequacy of single-locus barcoding across ecologically and phylogenetically disparate lineages, while taxon sampling remains geographically and phylogenetically uneven.
Implications: A stable, predictive classification of Basidiomycota will depend on expanded phylogenomic sampling of under-represented lineages, greater methodological consistency in divergence-time estimation, and continued integration of ultrastructural and ecological evidence with molecular phylogenies. Current frameworks provide a robust and largely convergent working hypothesis rather than a fully settled system.
Keywords: Agaricomycotina, basidiomycota, fungal phylogenomics, molecular systematics, nomenclature, pucciniomycotina, taxonomic classification, ustilaginomycotina