Dataset Information

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

ABSTRACT: 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. Thirteen viruses and viroids were identified in five Iranian grapevine cultivars, among which the grapevine red blotch virus and grapevine satellite virus were detected for the first time in Iranian vineyards. Grapevine leafroll-associated virus 1 (GLRaV1) and grapevine fanleaf virus (GFLV) were highly dominant in the virome. However, their frequency and abundance were somewhat different among grapevine cultivars. The results revealed a mixed infection of GLRaV1/grapevine yellow speckle viroid 1 (GYSVd1) and GFLV/GYSVd1 in grapevines that exhibited yellows and vein banding. We also propose a threshold of 14% of complete reconstruction as an appropriate threshold for detection of grapevine viruses that can be used as indicators for reliable grapevine virome profiling or in quarantine stations and certification programs.

SUBMITTER: Gholampour Z

PROVIDER: S-EPMC10891595 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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

Gholampour Zahra Z Zakiaghl Mohammad M Asquini Elisa E Moser Mirko M Gualandri Valeria V Mehrvar Mohsen M Si-Ammour Azeddine A

Viruses 20240129 2

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. Thirteen viruses and viroids were identified in five Iran ...[more]

PMID: 38399980

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Project description:Insensitivity and technical complexity have impeded the implementation of high-throughput nucleic acid sequencing in differential diagnosis of viral infections in clinical laboratories. Here, we describe the development of a virome capture sequencing platform for vertebrate viruses (VirCapSeq-VERT) that increases the sensitivity of sequence-based virus detection and characterization. The system uses ~2 million probes that cover the genomes of members of the 207 viral taxa known to infect vertebrates, including humans. A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform and used for solution-based capture of viral nucleic acids present in complex samples containing variable proportions of viral and host nucleic acids. The use of VirCapSeq-VERT resulted in a 100- to 10,000-fold increase in viral reads from blood and tissue homogenates compared to conventional Illumina sequencing using established virus enrichment procedures, including filtration, nuclease treatments, and RiboZero rRNA subtraction. VirCapSeq-VERT had a limit of detection comparable to that of agent-specific real-time PCR in serum, blood, and tissue extracts. Furthermore, the method identified novel viruses whose genomes were approximately 40% different from the known virus genomes used for designing the probe library. The VirCapSeq-VERT platform is ideally suited for analyses of virome composition and dynamics. IMPORTANCE : VirCapSeq-VERT enables detection of viral sequences in complex sample backgrounds, including those found in clinical specimens, such as serum, blood, and tissue. The highly multiplexed nature of the system allows both the simultaneous identification and the comprehensive genetic characterization of all known vertebrate viruses, their genetic variants, and novel viruses. The operational simplicity and efficiency of the VirCapSeq-VERT platform may facilitate transition of high-throughput sequencing to clinical diagnostic as well as research applications.

Project description:Background:Cucurbit aphid-borne yellows virus (CABYV) is among the most important yellowing viruses on cucurbits in Iran. The presence of CABYV has been previously reported from the major cucurbit growing areas in Iran, however, there are few studies concerning the detection of the different strains of this virus in the grower's fields, and especially, there is no report of the weed host plants near crop fields. Objectives: This study was done in order to detect the new strains of the CABYV polerovirus in cucurbits and the weed plants in the Lorestan province, Iran, as an introductory investigation for initiating a program of the breeding for resistance. Material and Methods: During a survey carried out in 2013-2014 in Lorestan province; Iran, 189 cucurbit and 261 weed samples were investigated for the presence of CABYV using RT-PCR. In addition, the phylogeny and nucleotide similarities were discussed on the basis of the partial nucleotide sequence of RNA dependent RNA polymerase (RdRP) gene. Results: The RT-PCR carried out on leaf samples revealed the infection with the CABYV in 43 cucumber and 12 weed samples. RT-PCR using strain specific primers detected the presence of the both common (C) and recombinant (R) strains of CABYV in the tested samples. On the basis of the phylogenetic analyses, the CABYV-C isolates from Iran were clustered into two distinct sub-populations (CI and CII), such that all the weed samples with two sequenced cucumber isolates were clustered in the CI sub-population. Meanwhile, a distinct sub-population of the isolates was clustered in the CABYV-R group showed a shared sequence identity of 97% to a Taiwanese isolate (JQ700306). Conclusions: This study has indicated the incidence of CABYV-R in the Southwest Asia; Iran for the first time. We were also able to show CABYV occurrence in Sysimbrium irio and Citrullus colocynthis from this area of the world. Identification of cucurbit infecting viruses and studying their distribution and potential reservoir hosts are important for developing successful control programs for virus disease management.

Dataset Information

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

Publications

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

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