Implementation of high-throughput sequencing of small RNAs for the sanitary certification of grapevine viruses in Spain
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PROVIDER: PRJEB42847 | ENA |
REPOSITORIES: ENA
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Project description:Grapevine microbiome (La Rioja, Spain) Raw sequence reads
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Project description:Our experiments investigated the effects of various known chemotherapeutic agents (2-thiouracil, ribavirin and zidovudine) on grapevine for the elimination of several different viruses and viroids. Viruses and viroids were identified by small RNA HTS in the mother plants of different grapevine cultivars, and RT-PCR verified the results. Among the tested agents, ribavirin had the broadest elimination effect on most viruses. It proved to be particularly effective against GFkV, GLRaV-4, GPGV and GRSPaV, however, as a single treatment it was not able to eliminate GFLV. In our experiments, ribavirin also showed very low efficacy against GLRaV-1 and GVA viruses. The application of 2-TU caused high phytotoxicity, with only 25% efficacy against GLRaV-4 among the viruses tested. Zidovudine failed to eliminate any of the viruses we tested. However, the combination of ribavirin and zidovudine was able to eliminate GFLV, though with low efficacy (12.5%). In contrast, the combination of ribavirin and 2-TU has been shown to be very effective against GRSPaV and GPGV. Compared to ribavirin, zidovudine and 2-thiouracil did not demonstrate significant virus elimination efficacy in the case of tested viruses. In our experiments ribavirin could not remove HSVd and GYSVd-1 viroids. To the best of our knowledge, no prior studies have been published the successful use of ribavirin or other chemotherapeutic agents against GLRaV-4, and this is the first publication of a successful application of 2-TU and zidovudine against grape viruses .
2025-12-31 | GSE283735 | GEO
Project description:Grapevine microbiome (Leiro, Ourense, Galicia/Spain)
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Project description:Meristem culture and somatic embryogenesis is an effective tool for virus elimination of vegetatively propagated crops including grapevine. While they both are proved to be useful to eliminate the main grapevine viruses their efficiency differs according to the virus and the variety. In our work we investigated their efficiency using small RNA high-throughput sequencing as virus diagnostic method. Field grown mother plants of four clones representing three cultivars, infected with different viruses and viroids were selected for sanitation via somatic embryogenesis and meristem culture. Our results show that the sanitation with SE was efficient against all of the presenting viruses, including grapevine Pinot gris virus, grapevine rupestris vein feathering virus and grapevine Syrah virus 1, having no data using somatic embryogenesis for their elimination. In case of other viruses and viroids such as GFkV, GRSPaV, GYSVd-1, HSVd this study confirms the findings of earlier researches, that SE is a possible way for elimination. While the efficiency of the elimination of different viruses was high, in case of viroids this ratio was lower. Our work demonstrated that efficiency of SE is comparable to the technically difficult meristem culture technique, and show promising way for the high demand of the production of virus-free grapevine in the future.
2020-12-31 | GSE159758 | GEO
Project description:In this study, grapevine cells control and elicited with 50 mM methylated cyclodextrins and 0.1 mM methyl jasmonate, that are known to accumulate extracellular resveratrol, were used to obtain membrane enriched fractions, specifically tonoplast and plasma membrane enriched fractions with the aim of finding candidate transporters of resveratrol. Label-free proteomic experiment was carried out using triplicates of the tonoplast and the plasma membrane enriched fractions. Protein identification was performed at the PROTEORED© proteomic facility of the University of Alicante (Spain) as detailed in the sample processing section.
2025-05-06 | PXD048454 | Pride
Project description:Effects of chemotherapy on the elimination of various viruses and viroids from grapevine
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Project description:Several pathogens infect grapevine, including viruses and viroids. Considering that there are no effective plant protection treatments against these pathogens and vineyards are cultivated through decades usage of high quality and pathogen-free propagation material (rootstocks and scions) is essential. Although presence of regulated pests is routinely checked using ELISA or rarely RT-PCR, these diagnostics methods can detect only particular pathogens moreover can fail to detect variant strains. High-throughput sequencing of small RNAs can be an effective, alternative method to avoid these disadvantages. Since for production of grafts, pathogen free cultivars and rootstocks must be used, 17 grapevine rootstock plantations and 2 rootstock variety collections were selected for characterisation of their virom by high throughput sequencing of virus derived small RNAs.
2020-02-24 | GSE130994 | GEO
Project description:Grapevine red blotch is a recently identified viral disease that was first recognized in the Napa Valley of California. Infected plants showed foliar symptoms similar to leafroll, another grapevine viral disease, on vines testing negative for known grapevine leafroll-associated virus. Later, the Grapevine red blotch virus (GRBV) was independently discovered in the US states of California and New York and was demonstrated to be the causal agent of red blotch disease. Due to its wide occurrence in the US, vector transmission and impacts on grape industry, this virus has the potential to cause serious economic losses. Despite numerous attempts, it was not possible to isolate or visualize viral particles from GRBV infected plants. Consequently, this has hampered the development of a serological assay that would facilitate GRBV detection in grapevine. We therefore decided to explore mass spectrometry approaches in order to quantify GRBV in infected plants and to identify potential biomarkers for viral infection. We present for the first time the physical detection on the protein level of the two GRBV genes V1 (coat protein) and V2 in grapevine tissue lysates. The GRBV coat protein load in leaf petioles was determined to be in the range of 100 to 900 million copies per milligram wet weight by using three heavy isotope labeled reference peptides as internal standards. The V1 copy number per unit wet tissue weight in leaves appeared to be about six times lower, and about 200-times lower in terms of protein concentration in the extractable protein mass than in petioles. We found a consistent upregulation of several enzymes involved in flavonoid biosynthesis in leaf and petiole extracts of GRBV-infected plants by label-free shotgun proteomics, indicating the activation of a defense mechanism against GRBV, a plant response already described for grapevine leafroll associated virus infection on the transcriptome level. Last but not least, we identified some other microorganisms belonging to the grapevine leaf microbiota, two bacterial species (Novosphingobium sp. Rr 2-17 and Methylobacterium) and one virus, Grapevine rupestris stem pitting associated virus.
2018-12-19 | PXD011002 | Pride