A Virome Scanning of Saffron (Crocus sativus L.) at the National Scale in Iran Using High-Throughput Sequencing Technologies

Saffron (<i>Crocus sativus</i> L.) is a vegetatively propagated crop of high economic and cultural value, potentially affected by viral infections that may impact its productivity. Despite Iran's dominance in global saffron production, knowledge of its virome remains limited. In this study, we conducted the first nationwide virome survey of saffron in Iran employing a high-throughput sequencing (HTS) approach on pooled samples obtained from eleven provinces in Iran and one location in Afghanistan. Members of three virus families were detected-<i>Potyviridae</i> (<i>Potyvirus</i>), <i>Solemoviridae</i> (<i>Polerovirus</i>), and <i>Geminiviridae</i> (<i>Mastrevirus</i>)-as well as one satellite from the family <i>Alphasatellitidae</i> (<i>Clecrusatellite</i>). A novel <i>Potyvirus</i>, tentatively named saffron Iran virus (SaIRV) and detected in three provinces, shares less than 68% nucleotide identity with known Potyvirus species, thus meeting the ICTV criteria for designation as a new species. Genetic diversity analyses revealed substantial intrapopulation SNP variation but no clear geographical clustering. Among the two wild Crocus species sampled, only <i>Crocus speciosus</i> harbored turnip mosaic virus. Virome network and phylogenetic analyses confirmed widespread viral circulation likely driven by corm-mediated propagation. Our findings highlight the need for targeted certification programs and biological characterization of key viruses to mitigate potential impacts on saffron yield and quality.