ClassifyITS: An R Package for assigning taxonomy to fungal ITS sequences using taxon-specific cutoff values

Fungi play a crucial role in global decomposition and nutrient cycling, but accurately identifying fungal species from environmental samples remains difficult. This difficulty arises from the variable evolutionary traits of fungal ITS sequences, incomplete representation of fungal diversity in reference databases, and the use of classifiers developed for more conserved prokaryotic markers.

To address these challenges, researchers have introduced ClassifyITS, an R package designed for alignment-based taxonomic classification of full-length fungal ITS sequences or individual ITS subregions (ITS1 or ITS2) based on taxon-specific sequence identity thresholds. ClassifyITS not only assigns taxonomic ranks but also generates summary statistics and visualization tools to aid in interpretation and quality control.

In a study using a deep subsurface fungal ITS dataset with many uncharacterized species, ClassifyITS demonstrated superior performance compared to standard classifiers SINTAX and DADA2. The new package achieved better agreement with expert-curated taxonomy and reduced the rates of both over and under classification of sequences.

The study highlights that taxonomic accuracy improves with sequence similarity to the reference database, underscoring the need for ongoing expansion and curation of fungal sequence databases. By offering a user-friendly and reproducible R workflow, ClassifyITS facilitates more precise biodiversity monitoring and enables enhanced downstream functional analysis of fungal communities.