Saffron (Crocus sativus L.) is a vital medicinal and aromatic plant which is affected by several viral diseases. To date, only one DNA virus infecting saffron, saffron dwarf virus (SaDV), has been identified. SaDV is a newly proposed species of the genus Mastrevirus in the family Geminiviridae which has been reported only in India. In this study, Iranian isolates of SaDV were identified through high-throughput sequencing, confirmed by PCR and Sanger sequencing. The complete genome length was 2725 nucleotides and it contained four ORFs encoding coat protein (CP), movement protein (MP), and two replication-associated proteins: RepA and Rep. The MP and CP are encoded on the virion-sense strand, while the RepA and Rep are encoded on the virion-antisense strand. Two intergenic regions were identified (LIR and SIR), with the LIR featuring a nonanucleotide origin of replication within a stem-loop structure. BLAST results revealed that the complete sequence of SaDV-IR shared 94.2% nucleotide identity with the only reported SaDV isolate from India (BK067261), suggesting a common origin for these isolates. The SaDV genome had the highest nucleotide identity, ranging from 52.4% to 54.5%, with the oat dwarf virus (ODV, Mastrevirus avenae) and wheat dwarf virus (WDV, Mastrevirus hordei) isolates, respectively. The phylogenetic trees based on replicase and whole genome sequences showed that SaDV clustered with ODV and WDV in a clade within the genus Mastrevirus, but formed a distinct sub-branch. To our knowledge, this is the first report of SaDV infecting saffron in Iran and the second report in the world.

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