Occurrence and molecular identification of Plantago tobamovirus 1 (Genus Tobamovirus) in Saffron (Crocus sativus L.) in Iran

Abstract

Saffron (Crocus sativus L.) plays a vital role in Iran's agricultural economy; however, viral infections pose a serious threat to its sustainable production. In this study, the presence ofPlantago tobamovirus 1 (PTV1) was identified and reported for the first time in Iranian saffron fields. Using virion-associated nucleic acid (VANA)–based metagenomics and 454 pyrosequencing, the virome of 161 leaf samples collected from three major saffron cultivation provinces was investigated. Approximately 74% of the reads were of viral origin, and sequences belonging to the family Tobamoviridae with 99.2–92.9% nucleotide identity to PTV1 were identified. Ten saffron samples tested positive for PTV1, and the presence of the virus was confirmed in three samples by RT-PCR and Sanger sequencing. Phylogenetic analyses based on the movement protein (MP) and RNA-dependent RNA polymerase (RdRp) genes revealed that the Iranian isolates clustered within the PTV1 clade but formed a distinct subclade, indicating their genetic divergence from reference isolates. The highest nucleotide identity of the Iranian isolate with the American isolate (OP594471) was approximately 98% for the RdRp gene and about 90% for the MP gene. A dN/dS ratio of less than one suggested the action of purifying selection on both genes. These findings provide the first molecular evidence of PTV1 infection in saffron in Iran and emphasize the necessity for monitoring emerging viruses and the role of weeds as potential reservoirs in the epidemiology of the virus.