Ontology highlight
ABSTRACT:
PROVIDER: PRJNA808843 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18085709_1.fastq.gz | Fastqsanger.gz | |||
| SRR18085709_2.fastq.gz | Fastqsanger.gz |
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Project description:New approaches to the production of certified varieties of apple trees using NGS diagnostics of pathogens
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Project description:Closed terminal buds of apple trees (Malus x domestica Borkh, Royal Gala and Castel Gala varieties) grown in commercial orchards were harvested during autumn and winter and exposed to cold treatments
2015-04-06 | GSE64717 | GEO
Project description:The purpose of this project is to examine the effects of rootstocks on the gene expression patterns in scions of apple trees. Gene expression patterns were examined in the Gala variety grafted onto seven different, commonly used rootstocks. These trees were grown in the greenhouse to limit environmental effects. Also, gene expression profiles were examined in three different varieties (Ambrosia, Melrose,and Gala) grafted onto B.9 rootstocks grown in the field. Keywords: apple, rootstock, graft, scion
2006-05-05 | GSE4762 | GEO
Project description:Fruit trees, as apricots, can be infected by and are constantly exposed to the attack of viruses. As they are propagated on a vegetative way, this risk is present not only at the field, where they exists for decades, but also during propagation. Metagenomic diagnostic methods, based on next generation sequencing, offer unique possibilities to reveal all the presenting pathogens in the investigated sample. Using small RNA NGS, a special fields of this technique, we tested leaf samples of different varieties of apricot in isolator house and at open air stock nursery. As a result, we identified Cherry Virus A (CVA) and Little Cherry Virus1 (LChV1) first time in Hungary. Gained results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral PCR products enabled us to investigate their phylogenetic relationships. Our results demonstrate, that small RNA NGS can offer a sensitive virus diagnostics method, moreover beside obligatory tested viruses we could detect CVA and LChV1. However as these pathogens haven’t been described in our country before, their role in symptom development and modification during coinfection with other viruses requires further investigations.
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Project description:The purpose of this project is to examine the effects of rootstocks on the gene expression patterns in scions of apple trees. Gene expression patterns were examined in the Gala variety grafted onto seven different, commonly used rootstocks. These trees were grown in the greenhouse to limit environmental effects. Also, gene expression profiles were examined in three different varieties (Ambrosia, Melrose,and Gala) grafted onto B.9 rootstocks grown in the field. Each sample is a pool of RNA from two different trees. RNA samples were isolated from 0.5 g of actively growing shoot tips, including leaf and stem tissues.
2006-05-05 | E-GEOD-4762 | biostudies-arrayexpress
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:We performed Illumina sequencing of sRNA libraries prepared from juvenile and reproductive phase buds from the apple trees. A large number of sRNAs exemplified by 33 previously annotated miRNAs and 6 novel members displayed significant differential expression (DE) patterns in juvenile and reproductive stages. The study provides new insight into our understanding of fundamental mechanism of poorly studied phase transitions in apple and other woody plants and important resource for future in-depth research in the apple development.
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Project description:Closed terminal buds of apple trees (Malus x domestica Borkh, Royal Gala and Castel Gala varieties) grown in commercial orchards were harvested during autumn and winter and exposed to cold treatments 18 biological samples, consisting of 9 pairs of replicates, were analysed in dye-swap. Samples are whole closed terminal buds. Biological replicates are buds from 2 different harvest year subjected to similar cold treatments. Samples with contrasting dormancy status in the same harvest year were compared in 8 dye-swap. Most samples were hybridized more than once in different combinations
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