Comprehensive analysis of the wheat leaf virome associated with Puccinia triticina isolates across Canada reveals high viral diversity and novel mycoviruses

Abstract Puccinia triticina Eriks. ( Pt ) is a basidiomycete fungal pathogen causing wheat leaf rust, a significant global threat to wheat production, leading to substantial yield losses in susceptible cultivars. Traditional management strategies, including planting resistant cultivars and deploying fungicides, are increasingly challenged by this pathogen’s rapid evolution and emergence of new virulent races. Recent interest has focused on mycoviruses, viruses that infect fungi, for their potential roles in biological control and influencing fungal population dynamics. This study investigates the virome of 117 Pt isolates collected across Canada when inoculated onto the susceptible wheat cultivar Thatcher. The total RNA was isolated from infected leaf tissues and metatranscriptome analysis followed by manual filtering steps revealed 37 unique viral species at the amino-acid (AA) level with the identity ranging from 30.4% to 100% across 6 viral families and unclassified viruses. High-throughput sequencing and RT-PCR amplification from germinated urediniospores mats confirmed the presence of putative mycoviruses, which could provide insights into their impact on the biology and epidemiology of Pt . Additionally, among the 37 viral species, we describe 17 novel viruses with high divergence based on the amino acid similarity from known viral species. This study reveals a diverse virome associated with P. triticina across Canada, highlighting the potential influence of mycoviruses on the pathogen’s biology, evolution, and epidemiology. This represents the first step toward opening new avenues for innovative management strategies against wheat leaf rust.