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Introduction More than 80 viral diseases of grapevines have been reported worldwide. The infectious degeneration disease complex causes growth reduction, stunting, shortening of internodes, bushy growth and decline in susceptible vines. Grapevine fanleaf viruses (GFLV), arabis mosaic virus (ArMV), grapevine deformation virus (GDefV), tomato ring spot virus (ToRSV) and tobacco ring spot virus (TRSV), which belong to the genus Nepovirus, are known to cause infectious degeneration. The genus Nepovirus has been divided into three subgroups A, B and C based on genome length, genomic organization, serological relationships, proteinase cleavage sites and the phylogenetic relationship of their coat protein (CP) gene. GDefV with the new name Nepovirus deformationis belongs to subgroup A of the genus Nepovirus and is closely related to ArMV and GFLV. Prevalence of GFLV in the vineyards of Iran raises the possibility that a mixed infection of GFLV and GDefV is also present in these areas. In Khorasan-Razavi Province, Iran's third-largest grape production center, research has addressed grape-affecting viruses with potential economic consequences, including reduced yield and product quality. Studying the distribution and genetic diversity of GDefV and other grape viruses is crucial for developing effective management and prevention strategies in the region's vineyards. In this study, GDefV was identified in the vineyards of Khorasan-Razavi province in Northeastern Iran and its complete genome was sequenced. In addition, the phylogenetic relationship of these isolates to other GDefV isolates deposited in GenBank was analyzed. Materials and Methods Samples from three grapevines were collected from a vineyard in Kashmer, Khorasan-Razavi Province; total RNA was extracted from the petiole of young leaves using the CTAB-PVPP method., GDefV and mixed infections of GDefV/GFLV were detected by PCR using specific primers. The PCR products were electrophoresed in a 1% agarose gel and sequenced. The miRNAs were extracted from grapevine petiole tissue using the modified CTAB method, and small RNA libraries were prepared using the TruSeq Small RNA Sample Prep Kit and sequenced on the Illumina Novaseq 6000 platform. After trimming the reads, contigs were generated using k-mer 15 in Velvet assembler 0.7.31. Contigs were verified using BLASTn and BLASTx in NCBI, and reconstruction of the GDefV genome from the NGS reads was performed using CLC Genomics Workbench (CLC Bio) software. Phylogenetic trees were generated in MEGA7 using the maximum likelihood (ML) method with 1000 replicates in the bootstrap test. The occurrence of possible recombinations in the GDefV genome was analyzed using the RDP v.6 package. Results and Discussion The samples showed leaf deformation, shortening of internodes, bushy growth, stunting and decline, but these symptoms are probably related to GFLV, and GDefV only causes leaf deformation in the infected vine. The PCR amplification and sequencing of a segment of the coat protein gene revealed a co-infection of GDefV and GFLV in the samples. GFLV is widely distributed in Iranian vineyards, GDefV has also been previously reported in the vineyards of northwestern Iran, but this is the first report of GDefV in the vineyards of Khorasan-Razavi Province. After refining the reads, approximately 15 million reads (92-99.7% of the original reads) remained for further analysis. The read sequences of each library were deposited in the Sequence Read Archive (SRA) under the accession number SAMN33747579-81. Three Iranian GDefV isolates obtained from three miRNA libraries were deposited in GenBank (accession numbers **-**). RNA1 and RNA2 of the three Iranian GDefV isolates had a length of 7386 and 3753 nucleotides, respectively. The RNA1 in GDefV had an open reading frame (ORF) of 6852 nucleotides in length, which started with the start codon AUG at position 288 and ended with the stop codons UAA or UAG at position 7142. The 5' end of the genome had 287 nucleotides long and contained two repeating sequences of 15 nucleotides that formed stem-loop structures. The length of the non-coding region at the 3' end had 244 nucleotides. Translation of RNA1 of the GDefV genome produces a polyprotein (p1) of 2285 amino acids (approximately 252 kda). The polyprotein p1 comprises the cofactor proteins proteinase, helicase, VPg, proteinase and polymerase with approximate weights of 45, 88, 3, 25 and 91 kDa, respectively. RNA2 also has one ORF, located between nucleotides 237 and 3560. This open reading frame also produces a 122 kDa polyprotein (P2) with 1108 amino acids. The second fragment of the GDeFV genome had 236 nucleotides as a 5'-noncoding region with three repeating sequences of 15 nucleotides that produced stem-loop structures with a 3-nucleotide loop and a 6bp stem. The 3'-noncoding region was also 193 nucleotides long. Polyprotein P2 comprised protein 2A, movement protein (MP) and coat protein (CP). The GDefV polyproteins had cysteine/alanine (C/A) and arginine/glycine (R/G) cleavage sites similar to those of the GFLV polyprotein. Comparison of the RNA1 sequences from three Iranian GDefV isolates with other GDefV isolates available in GenBank showed that the Iranian isolates had 88.1-92.2 % nucleotide identity with each other and 90.3-93.9 % with GenBank isolates at the nucleotide level. At the amino acid level, the Iranian isolates were 86.6-91.6 % identity with each other and 88.9-92.7 % with GenBank isolates. For RNA2, the Iranian isolates showed 89.4-92 % similar to each other and 89.6-94.2 % similar to GenBank isolates at the nucleotide level. The amino acid similarity between the Iranian GDefV isolates was 85-88.6 %. In the phylogenetic tree based on the nucleotide and amino acid sequences of RNA1 and RNA2 of the GDefV genome, the Iranian isolates of this study were clustered in a distinct clade than other GDefV isolates from Turkey (HE613269 and NC017939). GDefV was reported in 2003 and no further information is available on its distribution in vineyards around the world. GDefV has already been reported from Turkey and Iran, but the complete genome sequence of the Iranian GDefV isolate is being reported for the first time. Further studies on the population diversity of GDefV isolates in different regions of Iran are required to gain more insight into the mechanisms affecting the dynamics of GDefV populations. [ABSTRACT FROM AUTHOR]

Introduction: Soybean is a plant belonging to the Fabaceae family and is one of the most important oil seed in the world. The northern provinces of Iran are the main soybean cultivation regions in the country, but over the years, soybean podding disorder has reduced yield in this regions and caused up to 100% damage. The disorder is more severe in late planting farms, and symptoms can be observed as plant greening, accumulation of flowers and pods, abnormal pods, bud blight, and lack of seed in pod. The results of previous studies have shown the possible role of viruses in occurrence of soybean disorder. This research was conducted to investigate the Nepovirus effect on soybean yield and cultivars, and possible role on soybean podding disorder. Materials and Methods: 770 soybean sample from Golestan provinces were collected befor and after disorder appeared, and tested by DAS-ELISA and RT-PCR test for investigate the possible role of Nepovirus in disorder. The response of soybean cultivars to Nepovirus and soybean podding disorder, was evaluated in greenhouse and natural conditions. In greenhouse, 2 soybean cultivars (Katol, Saman) were inoculated mechanically at the 4-6 leaf stage. For comparison of soybean cultivars response to studied viruses and evaluation of possible role of Nepovirus on soybean podding disorder in natural condition, the experiment was performed in Golestan Agricuitural Research center as a split plot design with three factors: using net, virus inoculation and soybean cultivars with 3 replications in two years. Nepoviruses inoculated on specific plots on soybean plants at 4-6 leaf stages. ELISA and RT-PCR tests were used to ensure the plants infection with inoculated viruses, and growth indices were measured at physiological growth stage. Data were analyzed by two-way ANOVA, and the means were compared with LSD test at 5% confidence level, using SPSS software version 16.0. Results and Discussion: Comparing of viruse frequency in not disorder plants with podding disorder plants, did not show significant relationship between viruses and disorder incidence. In greenhouse, virus inoculation on soybean plants, caused chlorosis, stunt and systemic necrosis, but the typical symptoms of disorder such as severe falling of flowers, re-flowering, and plant greening did not show. In natural conditions, disorder was observed in all soybean cultivars, but disorder incidence was different among cultivars, and Williams variety showed less disorder in four treatments. The highest and lowest plant growth indices were observed in non-inoculation virus with use of net treatment and, virus inoculation with no use of net, respectively. Mechanical virus inoculation on different soybean cultivars, although reduced growth indices and soybeans yield, but had no significant effect on the podding disorder. In treatments with not controlling of sucker pests, the incidence of disorder was significantly higher than other treatments. Conclusion: Virus inoculation on soybean plants in greenhouse and natural conditions did not cause podding disorder syndrome. Viruses in soybean plants, reduce growth indices and aggravate disorder due to the stress they inflict on the soybean plant, but are not probably the cause of the disorder alone. In treatments with not controlling of sucker pests, disorder incidence was significantly higher, so the role of sucker pests was estimated effective and important. [ABSTRACT FROM AUTHOR]