Saffron (Crocus sativus) is a high-value perennial plant cultivated widely in Iran as a spice and medicinal plant. Several pathogens including viruses can infect saffron and decrease its quality and quantity. Precise and reliable detection is a critical aspect of disease management in viral diseases because of the lack of commercially available chemicals against plant viruses. Nowadays, high throughput sequencing (HTS) has been considered as a routine technology for detection of known and novel viruses in commercial plants. In this study, using HTS data, saffron latent virus (SaLV) and prunus virus T (PrVT) were identified in transcriptomic data of stigma of saffron and near complete genome of these viruses were obtained. The near complete genome of SaLV isolate had 98.3% nucleotide sequence identity with the only available isolate in GenBank. The complete genome of saffron isolate of PrVT shared 42.9 (potato virus T isolate Peru) – 76.9 % (olive virus T isolate GR168) nucleotide sequence identity with those of tepoviruses available in GenBank. In a phylogenetic tree, the PrVT isolate clustered with two Greece OlVT isolates along with an isolate of PrVT. To the best of our knowledge, this is the first report of PrVT infection in saffron worldwide.
