Viral diseases infect many commercially important plants worldwide, including iris, and impair their production and quality. Here, the first genomic sequence of narcissus latent virus (NLV-IR) from naturally infected iris plants (Iris versicolor) in Iran was determined using RNA deep sequencing, and confirmed by RTPCR followed by Sanger sequencing. The genomic RNA of NLV-IR was 8236 nucleotides in length; excluding the 3′-poly(A) tail and contained a single ORF of 7872 nucleotides encoding a large polyprotein of 2624 amino acids. Its genomic structure was typical of macluraviruses, which lack the P1 protein, N-terminal HC-Pro, and DAG, PTK, and KITC motifs for aphid transmission. The complete genome sequence of NLVIR showed nt identities of 81.52% and 81.39% (90.36% aa identity) with two publicly available NLV sequences from the Netherlands and Australia, respectively. The low nt and aa sequence identity with known NLV isolates suggested that it was most likely a novel strain. Sequence comparisons showed 77.44–98.20% and 78.45–99.33% sequence identity at nt and aa level, respectively, of the cp gene of NLV isolates from Iran and other parts of the world. The genetic diversity of NLV isolates was considerable, and no recombination events were found among these sequences. Based on phylogenetic analyses of cp gene sequences, all 26 NLV isolates clustered into two main phylogroups which had highly significant genetic differentiation with an FST value of 0.917. The phylogenetic grouping and geographic location of the isolates had a limited correlation. Purifying selection was detected at the majority of polymorphic sites although a few codons were under positive selection. With exception of East Asian population which was strongly differentiated from European population, almost no significant differentiation was found among geographic populations. This indicated that gene flow can play an important role in differentiation and distribution of genetic diversity among populations. These genetic features provide crucial information for the long-term and effective management of NLV.

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