Molecular Identification of Oomycetes Reveals Nuclear - Mitochondrial Marker Discordance in Saprolegnia in the Midwest United States

The oomycete genus Saprolegnia includes both saprophytic and pathogenic species that threaten freshwater ecosystems and aquaculture. Despite its importance, the molecular diversity and evolutionary relationships in the Midwest United States (US) remain unresolved. Multilocus approaches using ITS and COX1 markers, we analyzed 47 isolates from aquaculture and natural freshwater habitats to assess species diversity and evolutionary relationships. Phylogenetic analyses identified nine Saprolegnia species and revealed widespread mitochondria–nuclear discordance. Notably, a high-risk S. parasitica S2 phylotype displayed a hybrid-like signature possessing S. parasitica nuclear identity with S. delica COX1 mitochondrial sequence, consistent with historical and ongoing hybridization. These findings highlight the complexity of Saprolegnia evolution and the limitations of single-locus identification. While resolving mito-nuclear discordance requires multilocus or genome-scale approaches, ITS sequencing remains the most effective strategy for broad-scale species delimitation and environmental monitoring. This study provides the first molecular survey of Saprolegnia diversity across the Ohio - Michigan - Indiana region and establishes a foundation for improved taxonomy and disease management.