Several viruses affect iris plants worldwide, and are major constraints in commercial production due to serious economic losses. The first genomic sequences of two potyviruses, namely, Iris Severe Mosaic Virus (ISMV) and Iris Mild Mosaic Virus (IMMV) from naturally infected iris plants (Iris versicolor) in Iran were determined using RNA deep sequencing and RT-PCR followed by sequencing of amplicons. Both viruses (ISMV-Ir and IMMV-Ir) had a typical potyvirus genetic organization, with a large open reading frame translated as a polyprotein, including nine autocatalytic cleavage sites, and a putative smaller protein P3N-PIPO. Phylogenetic analyses and sequence comparisons revealed close relationships between ISMV and members of group Onion Yellow Dwarf Virus (OYDV) of the genus Potyvirus. The ISMV-Ir showed > 92% nucleotide (nt) identity (> 96% amino acid (aa) identity) to the three previously reported ISMV isolates, the highest with the Japanese isolate J (94.10% nt identity, 97.41% aa identity) and the lowest with Chinese isolate BJ (92.73% nt identity, 96.77% aa identity). IMMV-Ir belonged to the Chilli Veinal Mottle Virus (ChVMV) group of potyviruses, had 82.36% nt identity (91.25% aa identity) with the BC32 isolate, and 75.55% nt identity (83.59% aa identity) with the WA-1 isolate from Australia. The genetic distance among IMMV polyprotein-coding genomic sequences or gene-specific sequences indicated a high genetic divergence of these isolates. Our analysis indicated that natural selection has contributed to the evolution of isolates belonging to the two identified potyviruses. The information on genomic sequences presented in this study will improve our understanding of virus function and pathogenicity leading to better control of the disease.

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