Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

NGS of virus derived small RNAs as a diagnostics method used to determine viromes of Hungarian vineyards

ABSTRACT: NGS of virus derived small RNAs as a diagnostics method used to determine viromes of Hungarian vineyards

PROVIDER: PRJNA415982 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6224670.fastq.gz	Fastqsanger.gz
	SRR6224680.fastq.gz	Fastqsanger.gz
	SRR6224671.fastq.gz	Fastqsanger.gz
	SRR6224681.fastq.gz	Fastqsanger.gz
	SRR6224672.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

NGS of virus derived small RNAs as a diagnostics method used to determine viromes of Hungarian vineyards

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.

2018-04-05 | GSE106240 | GEO

The detection of Prunus virus F and its distribution in Hungarian sour cherry orchards

Project description:Viromes of sour and sweet cherry trees in Hungarian germ line collections were surveyed using small RNA HTS as an unbiased method. RNA from leaf samples of different cultivars were purified and used to produce seven pools from which small RNA HTS libraries were prepared. The sequenced reads were analyzed using bioinformatic methods to revel the presence of viruses in the samples. Presence of the viruses were validated using RT-PCR.

2024-10-31 | GSE233558 | GEO

small RNA NGS based diagnostic survey of Hungarian grapevine rootstock plantations

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

Hungarian BAM files

Project description:Hungarian BAM files

| PRJEB20905 | ENA

Chilean vineyards

Project description:ITS2 seqeuncing of 34 chilean vineyards

| PRJEB75257 | ENA

Progressive retinal atrophy in the Hungarian Puli

Project description:Progressive retinal atrophy (PRA) is a common cause of blindness in many pure and mixed breed dogs (Canis lupus familiaris). The typical onset of PRA begins with gradual night vision loss followed by day vision loss due to the death of rod and cone receptors, respectively. There are currently no mutations or genes reported to be causative or associated with PRA in the Hungarian Puli. In this study, we use an extensive list of 53 known PRA genes to screen for putative causal variants in this breed of dog.

2016-10-31 | GSE87642 | GEO

Soil from different vineyards

Project description:Soil from different vineyards Metagenome

| PRJNA907731 | ENA

small RNA NGS based diagnostic survey of Hungarian grapevine rootstock plantations

Project description:small RNA NGS based diagnostic survey of Hungarian grapevine rootstock plantations

| PRJNA542259 | ENA

Lake Baikal Viromes

Project description:Lake Baikal Viromes Raw sequence reads

| PRJNA547700 | ENA

Mediterranean Viromes

Project description:Marine viromes from a depth profile at the Mediterranan sea