Application of High-Throughput Sequencing for Comprehensive Virome Profiling in Grapevines Shows Yellows in Iran.

A comprehensive study on the whole spectrum of viruses and viroids in five Iranian grapevine cultivars was carried out using sRNA libraries prepared from phloem tissue. A comparison of two approaches to virus detection from sRNAome data indicated a significant difference in the results and performance of the aligners in viral genome reconstruction. The results showed a complex virome in terms of viral composition, abundance, and richness.

Assessment of the phenotypic and genotypic diversity of endophytic strains of Bacillus and closely related genera from Carpinus betulus in the Hyrcanian forests of Iran.

Background: Identification and characterization of the endophytic microorganism, is gaining their underestimated significance in influencing health, performance, and other biological attributions of plants in general and forest tree species in particular. Because of the scarcity of information on the endophytic microbiome of the Hyrcanian forests species, including hornbeam (Carpinus betulus L.) trees, as a major constituent thereof, the present study aimed at the identification and partial characterization of the endophytic Bacillus species of Carpinus betulus as the first step in this context.

First report of infecting saffron in Iran.

Saffron () is widely used as an important herbal medicine crop worldwide. Iran is the largest producer and exporter of saffron in the world. (TuMV) is a species of the genus , which infects a wide range of plants species.

Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of Vinca minor and Wisteria sinensis in Iran: with Implications for the Genetic Structure of the Virus.

Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS.

Identification of garlic-infecting leek yellow stripe virus through deep-sequencing analyses from Iran.

Unlabelled: In the study presented here, the first complete genome sequence of (LYSV) designated as isolate LYSV-AE65 from Southwest of Iran, was reported. The small RNA deep sequencing analysis showed that, the Iranian isolate has a full RNA genome of 10,142 nucleotide in length (Except for poly (A) tail) and it was shared 77.91-92.

Whole genome characterization of wisteria vein mosaic virus from Iran and its relationship to other members of bean common mosaic virus group.

Unlabelled: To date, the complete genome of two wisteria vein mosaic virus (WVMV) has been sequenced worldwide. Here, the genomic sequence of WVMV isolated from in Iran was determined for the first time, using deep RNA sequencing and RT-PCR followed by Sanger sequencing. The sequence was 9694 nucleotides in length; excluding the 3'-poly(A) tail and contained a single open reading frame of 9279 nucleotides encoding a large polyprotein of 3092 amino acids and predicted molecular weight of 35,368 KDa.

Molecular characterization of two highly divergent Iranian johnsongrass mosaic virus isolates from .

Iranian johnsongrass mosaic virus (IJMV, genus , family ) is one of the most prevalent viruses causing maize mosaic disease in Iran. In this study, the complete genomes (9,618 and 9,543 nucleotides) of two highly divergent IJMV isolates (Maz2 and Maz3) were obtained from the metagenomic analysis of RNAs using Illumina sequencing. The genome contained a single open reading frame (9,165 nucleotides) encoding a polyprotein of 3,054 amino acids, flanked by a 5'-untranslated region (UTR) of 216 and 143 nucleotides and a 3'-UTR of 237 and 235 nucleotides.

Analysis of the molecular and biological variability of Zucchini yellow mosaic virus isolates from Iran and Iraq.

During the growing season of 2018, several field-grown cucurbit plants in different parts of Iraq and Iran were surveyed for the presence of zucchini yellow mosaic virus (ZYMV), using two degenerate primer pairs (CIF/Rev and NIb2F/3R) targeting the two separated partial regions of the potyvirus genome (CI and NIb respectively). 7 out of 20 samples were confirmed to be infected with ZYMV. Phylogenetic analyses based on the CI gene grouped all Iranian and two Iraqi (ZYMV1 and ZYMV2) isolates together with isolates from the Middle East in the subgroup (AI), whereas the other Iraqi (ZYMV3 and ZYMV4) isolates were clustered in the subgroup (DI), which was only consisted of American isolates.

Complete Genomic Characterization of Two Beet Soil-Borne Virus Isolates from Turkey: Implications of Comparative Analysis of Genome Sequences.

Sugar beet (Beta vulgaris L.) is known as a key product for agriculture in several countries across the world. Beet soil-borne virus (BSBV) triggers substantial economic damages to sugar beet by reducing the quantity of the yield and quality of the beet sugars.

Genetic diversity and biological characterization of sugarcane streak mosaic virus isolates from Iran.

Sugarcane streak mosaic virus (SCSMV; genus , family ) is a major causal agent of sugarcane mosaic disease in Asia. A survey of SCSMV was conducted in cultivated fields in Khuzestan province, southwestern Iran. Sixty-five sugarcane leaf samples showing mosaic symptoms were collected and investigated by RT-PCR.

Nucleotide sequence analyses of coat protein gene of peanut stunt virus isolates from alfalfa and different hosts show a new tentative subgroup from Iran.

Alfalfa cultivars grown in 14 provinces in Iran were surveyed for the relative incidence of peanut stunt virus (PSV) during 2013-2016. PSV were detected in 41.89% of symptomatic alfalfa samples and a few alternate hosts by plate-trapped antigen ELISA.

Occurrence and Evolutionary Analysis of Coat Protein Gene Sequences of Iranian Isolates of .

(SCMV) is one of the most damaging viruses infecting sugarcane, maize and some other graminaceous species around the world. To investigate the genetic diversity of SCMV in Iran, the coat protein (CP) gene sequences of 23 SCMV isolates from different hosts were determined. The nucleotide sequence identity among Iranian isolates was more than 96%.

Iranian johnsongrass mosaic virus: the complete genome sequence, molecular and biological characterization, and comparison of coat protein gene sequences.

Iranian johnsongrass mosaic virus (IJMV) is one of the most prevalent viruses causing maize mosaic disease in Iran. An IJMV isolate, Maz-Bah, was obtained from the maize showing mosaic symptoms in Mazandaran, north of Iran. The complete genomic sequence of Maz-Bah is 9544 nucleotides, excluding the poly(A) tail.

The complete genome sequences of two naturally occurring recombinant isolates of Sugarcane mosaic virus from Iran.

Sugarcane mosaic virus (SCMV) is the most prevalent virus causing sugarcane mosaic and maize dwarf mosaic diseases. Here, we presented the first two complete genomic sequences of Iranian SCMV isolates, NRA and ZRA from sugarcane and maize. The complete genome sequences of NRA and ZRA were, respectively, 9571 and 9572 nucleotides (nt) in length, excluding the 3'-terminal poly(A) tail.

Molecular variability in the cysteine rich protein of potato virus M.

The potato virus M (PVM), belonging to the genus Carlavirus, is a worldwide endemic pathogen in potato fields. p11 is an 11-16 kDa protein encoded by the last open reading frame of PVM which contains cysteine rich proteins (CRPs) motif. CRPs have been identified as suppressors of gene silencing.

Genetic structure and molecular variability of potato virus M populations.

To investigate the genetic diversity of potato virus M (PVM; genus Carlavirus, family Betaflexiviridae), the complete nucleotide sequence of the coat protein gene of 30 PVM isolates from a major potato-growing region in Iran were determined. Phylogenetic analysis of these Iranian PVM isolates together with those available in the GenBank database suggested two divergent evolutionary lineages that did not reflect the origin of the isolates, and these were designated as PVM-o and PVM-d. Examination of the genetic variability of the coat protein of Iranian isolates and their counterparts whose sequences are available in the Genbank database revealed 16 genotype groups in the PVM population.

Diversity of beet curly top Iran virus isolated from different hosts in Iran.

Beet curly top Iran virus (BCTIV) is a major pathogen of sugar beet in Iran. In order to study diversity of BCTIV, we sampled 68 plants in Iran during the summer of 2010 with curly top disease symptoms on beans (Phaseolus vulgaris), cowpeas (Vigna unguiculata), tomatoes (Solanum lycopersicum L.), sea beets (Beta vulgaris subsp.

A full-length infectious clone of beet soil-borne virus indicates the dispensability of the RNA-2 for virus survival in planta and symptom expression on Chenopodium quinoa leaves.

For a better understanding of the functionality and pathogenicity of beet soil-borne virus (BSBV), full-length cDNA clones have been constructed for the three genomic RNAs. With the aim of assessing their effectiveness and relative contribution to the virus housekeeping functions, transcripts were inoculated on Chenopodium quinoa and Beta macrocarpa leaves using five genome combinations. Both RNAs-1 (putative replicase) and -3 (putative movement proteins) proved to be essential for virus replication in planta and symptom production on C.