Ontology highlight
ABSTRACT:
PROVIDER: PRJNA667593 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12778419.fastq.gz | Fastqsanger.gz | |||
| SRR12778420.fastq.gz | Fastqsanger.gz | |||
| SRR12778421.fastq.gz | Fastqsanger.gz | |||
| SRR12778422.fastq.gz | Fastqsanger.gz | |||
| SRR13052612.fastq.gz | Fastqsanger.gz |
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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.
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Project description:As virus diseases cannot be controlled by traditional plant protection methods the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomics approaches used for virus diagnostics, offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, why their usage can reduce the risk of using infected material for a new plantation. Here we used a special field, deep sequencing of virus derived small RNAs, of this high throughput method for virus diagnostics and determined viromes of vineyards in Hungary. With NGS of virus derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which have never been described in Hungary before. Virus presence didn’t correlated with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections mostly caused by the usage of infected propagating material. Our results, validated by other molecular methods, highlighted further questions to be answered before these method can be introduced as a routine, reliable test for grapevine virus diagnostics.
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Project description:NGS of virus derived small RNAs as a diagnostics method used to determine viromes of Hungarian vineyards
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Project description:During a proof-of-concept study, virome of millet, grown as weed was determined by small RNA HTS. As a result, from the pools of 20 randomly collected millet samples collected at two locations, we identified the presence of three viruses, two of them first time in Hungary. Based on our results we could only suspect that these viruses: wheat streak mosaic virus (WSMV), barley stripe mosaic virus (BYSMV) and barley virus G (BVG) could have been overwintered in millet or other monocotyledonous weeds growing at these fields. As a follow-up research, in the summer of 2021, we collected symptomatic leaves of several monocotyledonous plants at the same fields. This time the sampling was done in July. From the samples, small RNA HTS was carried out.
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