Taxonomic validation of Saccharomycotina yeast genome assemblies through type-material-anchored BLAST-based average nucleotide identity analysis at the NCBI

The extensive genomic resources available for Saccharomycotina yeasts, including assemblies derived from type material, make this group well suited for genome-based taxonomic verification. This study evaluates the effectiveness of type-material-informed Average Nucleotide Identity (ANI) analysis for verifying the taxonomic assignments of Saccharomycotina genome assemblies. Public yeast genome assemblies were compared against type material assemblies using an alignment-based ANI workflow. Operational thresholds were established, and results were compared with DNA-DNA hybridization and FastANI analyses. Assemblies were evaluated by best-match status and coverage, and problematic type assemblies were flagged for further review. A 95% ANI threshold yielded high concordance with declared species assignments among query-to-type comparisons. Cases of high similarity between different species and hybrid genomes were identified, highlighting the need for expert taxonomic review in certain instances. The alignment-based ANI showed a strong correlation with traditional DNA-DNA reassociation values and agreed closely with FastANI for highly alignable assemblies. Type-material-informed ANI is a reliable tool for automated taxonomic verification of yeast genome assemblies, but its effectiveness depends on the availability and quality of type assemblies and accurate metadata. The approach enables continuous quality control and supports broader application in fungal taxonomy, with recommendations for improving reference coverage and data submission practices.