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High-throughput sequencing of small RNAs in Vitis vinifera

ABSTRACT: Vitis vinifera endogenous small RNAs Size fractionated small RNA from total RNA extracts of Vitis vinifera leaves, inflorescences, tendrils and small berries were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

ORGANISM(S): Vitis vinifera

SUBMITTER: Simon Moxon

PROVIDER: E-GEOD-18405 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis.

Pantaleo Vitantonio V Szittya Gyorgy G Moxon Simon S Miozzi Laura L Moulton Vincent V Dalmay Tamas T Burgyan Jozsef J

The Plant journal : for cell and molecular biology 20100601 6

In plants, microRNAs (miRNAs) comprise one of three classes of small RNAs regulating gene expression at the post-transcriptional level. Many plant miRNAs are conserved, and play a role in development, abiotic stress responses or pathogen responses. However, some miRNAs have only been found in certain species. Here, we use deep-sequencing, computational and molecular methods to identify, profile, and describe conserved and non-conserved miRNAs in four grapevine (Vitis vinifera) tissues. A total o ...[more]

PMID: 20230504

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High-throughput sequencing of small RNAs in Vitis vinifera

Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Vitis vinifera tissues (including leaves, flowers and berries). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study. Small RNA libraries were derived from leaves flowers and berries of Vitis vinifera. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Gabriele Di Gaspero for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

2011-09-29 | E-GEOD-32479 | biostudies-arrayexpress

microRNA-target RNA pairs revealed by Parallel analysis of RNA ends in Vitis vinifera

Project description:Vitis vinifera RNA degradome Isolated polyadenylated RNA from total RNA extracts of Vitis vinifera leaves, were ligated to 5'-adapter that include san MmeI recognition site. The ligated products were purified again, reverse transcribed and cleaved with MmeI. The 5' fragments were purified from gel and to a 3'- dsDNA adapter and PCR amplified. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

2010-04-29 | E-GEOD-18406 | biostudies-arrayexpress

Novel functional microRNAs from virus-free and infected Vitis vinifera plants under water stress.

Project description:Size fractionated small RNA from total RNA extracts of Vitis vinifera leaves were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit Please see www.illumina.com for details of the sequencing technology.

2016-02-02 | GSE63244 | GEO

High-throughput sequencing of small RNAs in Vitis vinifera

Project description:Vitis vinifera endogenous small RNAs

2010-04-29 | GSE18405 | GEO

Vitis vinifera Transcriptome or Gene expression

Project description:Seedless varieties are of particular importance to the table-grape and raisin industries. Gibberellin (GA) application is widely used in the early stages of seedless berry development to increase berry size and economic value. However, the underlying mechanism of GA induction of berry enlargement is not well understood. Here, RNA-sequencing analysis of âCentennial Seedlessâ (Vitis vinifera L.) berries treated with GA3 12 days after flowering is reported.

2014-12-05 | E-MTAB-4247 | biostudies-arrayexpress

High-throughput sequencing of small RNAs in Vitis vinifera

2011-09-30 | GSE32479 | GEO

Distribution of Small RNAs Along Transposable Elements in Vitis vinifera During Somatic Embryogenesis

Project description:In the present study we have generated a parallel analysis of the 5' RNA ends (PARE) referred to polyadenylated RNAs in somatic embryos from in vitro culture of immature anthers of Vitis vinifera. PARE analysis include also a shortRNA analysis of same material. We have submitted the sRNAseq to mirPROOF and miRCAT (srna_workbench software at http://srna-workbench.cmp.uea.ac.uk) in order to recognize known and putative novel miRNAs, respectively that could be present in somatic embryos. In addition, aRNAs and PARE libraries were integrated in order to identify those 5' RNA ends that could be explained by sRNAs (i.e. identify transcripts that could be cleaved by sRNAs). We have used publicly available annotations and we gained a deep insight into the gene families and the transcriptional regulation mediated by miRNAs in V. vinifera somatic embryos. Gene expression is finely regulated to specific paralogues in gene families such as the NADPH-dependent diflavin oxidoreductase, Phosphoserine aminotransferase, Ethylene-responsive transcription factors, glutathione S-transferase par C, just to name a few. We have indeed characterized at least 4,000 mRNA targets. Size fractionated small RNA from total RNA extracts of somatic Embryos cv. "Brachetto" were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit, Illumina. Please see www.illumina.com for details of the sequencing technology. PARE libraries were generated starting from Poly(A) fraction. The protocol used have been previously described in German et al., 2009, Nature protocols. Please see www.illumina.com for details of the sequencing technology.

2024-04-22 | GSE150881 | GEO

Red vs white skins of Vitis vinifera cv. ‘Bequignol Noir’

Project description:Transcriptome analysis of red vs white berry skin parts of variegated Vitis vinfera ‘Bequignol Noir’ berries.

2023-08-17 | GSE241123 | GEO

microRNA-target RNA pairs revealed by Parallel analysis of RNA ends in Vitis vinifera

Project description:Vitis vinifera RNA degradome

2010-04-29 | GSE18406 | GEO

Somatic embryogensis of Vitis vinifera exhibits a transcriptomic hourglass pattern

Project description:The objective of the study was to uncover the developmental dynamics in the artificially induced somatic embryogenesis of Vitis vinifera on the transcriptome level.

2024-07-23 | GSE234231 | GEO

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