For the first time, the nearly complete genome sequence of Onion Yellow Dwarf Virus (OYDV) was found in Iran from garlic (Allium sativum L.) by deep RNA sequencing. Iranian OYDV isolate (IR-Kh2/ MN528769) consists of 10,519 nucleotides (nt), excluding the poly (A) tail and encodes a polyprotein of 3,403 amino acids (aa), flanked by 5’ and 3’ Untranslated Regions (UTRs) of 93 and 214 nt, respectively. Pairwise sequence comparisons showed that IR-Kh2 shares 72.76-96.42% nt sequence identity at the complete genome level and 74.84-97.39% nt sequence identity at the polyprotein level, respectively. According to the phylogenetic analysis, the OYDV isolates were divided into two main groups based on the complete genome sequence and the Iranian OYDV isolate cluster together with the Australian (MS/SW1), Spanish (SG1), Chinese (G78 and G37-2), and Indian (RR1) isolates. Furthermore, a genetic recombination analysis was also performed, in which a putative recombination event was detected in the Nuclear Inclusion body b (NIb) gene.

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