Iris yellow spot virus (IYSV) is a member of the Eurasian phylogenetic group of the genus Orthotospovirus. Similar to other species in the genus, the viral particles contain three genomic fragments: small (S), medium (M), and large (L) RNAs. In the present study, the complete nucleotide sequence of the small fragment (S) RNA of two IYSV isolates from leek (Allium ampeloprasum ) (IYSV-Le1M) and onion (A. cepa) (IYSV-O2K) and the non-structural gene of the M RNA of the IYSV-Le1M isolate were determined. The results showed that based on nucleocapsid (N), small (NSs), and medium (NSm) RNA fragment non-structural genes, the isolates of Markazi Province are more closely related to each other than other IYSV isolates. However, the intergenic region (IGR) of the two isolates showed significant structural differences compared to other sequenced IYSV isolates. The IGR of the IYSV-Le1M isolate was longer than those of other IYSV isolates studied, while, for IYSV-O2K isolate, it was 440 nucleotides shorter. It was also found that for Indian and Dutch IYSV isolates, the IGR was 31 and 22 nucleotides shorter than that in the IYSV-Le1M isolate. These findings provide new information about the genetic diversity and phylogeny of IYSV isolates.
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