2025/11/06 by Benjamin Bolduc, Olivier Zablocki, Dann Turner +5 · 1 voice · 5 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Bacteriophages and microbial interactions #Biological classification #Environmental DNA in Biodiversity Studies #Eukaryote #Genome #Genomics and Phylogenetic Studies #Metagenomics #Prokaryote #Scalability #Taxonomy (biology) #Virus classification
paper · pdf · doi:10.1101/2025.11.06.686974
published in bioRxiv (Cold Spring Harbor Laboratory) (Cold Spring Harbor Laboratory)
openalex publication_date 2025/11/06 · openalex created_date 2025/11/07 · openalex updated_date 2026/08/04
Abstract Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes with multiple evolutionary origins, and lack of a universal barcode gene. While virus ecogenomics has expanded access to and understanding of the virosphere, available classification tools poorly scale to modern discovery-based datasets, lack taxonomic resolution, and/or are unable to classify novel sequence space. Here we develop, benchmark, and release vConTACT3, a machine learning-based tool that improves scalability and accuracy, adds extensive user-requested features, expands classification to both eukaryote and prokaryote viruses for 4/6 officially recognized realms, and establishes accurate hierarchical taxonomy from genus to order. Application to 48,069 public virus genomes provided new taxonomy assignments for thousands of taxa, revealed support for fewer taxonomic ranks than currently available, and systematically identified taxonomically problematic areas across the virosphere.