م.زکی عقل

Squash Mosaic Virus (SqMV) is a Comovirus that infects many cucurbit crops worldwide. In this study, the first two complete genome sequences of SqMV (BSQ and TSQ) from Iran were determined. The RNA genomes of isolates BSQ and TSQ were, respectively, 5,754 and 5,755 (RNA1) and 3290 and 3271 (RNA2) nucleotides (nt) in length, excluding the 3'-terminal poly (A) tail. RNA1 of both isolates encodes a single polyprotein of 1858 amino acids (aa). The identity between the two Iranian isolates (BSQ and TSQ) was 94.24% nt and 94.82% aa for RNA1 and 88.80% nt and 89.50% aa for RNA2. In comparison to other SqMV isolates, BSQ and TSQ shared the highest nucleotide sequence identities of 95.12 % to 93.56 % (RNA1), and 87.59 % to 87.19 % (RNA2), respectively, with the Spanish isolate (RZ-SqMV). Phylogenetic analysis based on complete genome sequences reveals that SqMV isolates cluster into three distinct groups. BSQ was clustered alongside a Spanish isolate in one group and TSQ was separately clustered with a Chinese and US isolates in another group. Recombination analysis revealed that BSQ (RNA1, 2) and TSQ (RNA2) were putative recombinants. BSQ had 6 recombination sites within 5'-UTR, helicase, protease, RdRP (in RNA1), SCP and 3'-UTR (in RNA2) regions, whereas TSQ had 4 recombination sites within 5'-UTR, MP (two breaking points) and LCP region.

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. Complete coding sequence of the Iranian isolate of OYDV (MN528769) consists of 10,212 nucleotides (nt), encodes a polyprotein with 3,403 amino acids (aa). Pairwise sequence comparisons showed that IR-Kh2 shares 74.84-97.39% identity at the nt level and 75.67-98% identity at the amino acids level, respectively with other OYDV isolates deposited in the GenBank previously. According to the phylogenetic analysis, the OYDV isolates were divided into two main groups based on the coding sequence of genome 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.

The common cutworm, Agrotis segetum, is a serious soil pest of many vegetable and field crops all over the world. Morphological identification of Agrotis species is predominantly performed on adults due to the deficiency of adequate identification keys for immature stages. In international trade, the immature life stages are frequently being intercepted at point of inspection, challenging the possibilities of morphological identification. To realize a rapid and reliable identification for all stages of A. segetum, a TaqMan real-time Polymerase Chain Reaction (PCR) was developed based on the mitochondrial Cytochrome Oxidase I (COI) gene. All specimens of A. segetum (including various life stages) were detected and no cross-reactivity was observed with 5 non-target Agrotis species in the specificity tests. The tests showed to be repeatable, reproducible, and robust. The assay performed equally well with crushed insects and purified DNA, so, the efficiency was added by removing DNA extraction step. The method has proven to be suitable tools for routine identification of all life stages of A. segetum considering the speed, specificity, as well as sensitivity of the assay.