Vitis vinifera
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA309385 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3110967.fastq.gz | Fastqsanger.gz | |||
| SRR3110968_1.fastq.gz | Fastqsanger.gz | |||
| SRR3110968_2.fastq.gz | Fastqsanger.gz | |||
| SRR3110969_1.fastq.gz | Fastqsanger.gz | |||
| SRR3110969_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
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Project description:Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.
2021-08-27 | GSE164584 | GEO
Project description:Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.
2021-08-27 | GSE164583 | GEO
Project description:Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.
2021-08-27 | GSE164582 | GEO
Project description:MicroRNAs (miRNAs) play a important part in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice and other plants. However, the number of miRNAs discovered in grape is relatively low and little is known about miRNAs responded gibberellin during fruit germination. In this study, a small RNA library from gibberellin grape fruits was sequenced by the high throughput sequencing technology. A total of 16,033,273 reads were obtained. 812,099 total reads representing 1726 unique sRNAs matched to known grape miRNAs. Further analysis confirmed a total of 149 conserved grapevine miRNA (Vv-miRNA) belonging to 27 Vv-miRNA families were validated, and 74 novel potential grapevine-specific miRNAs and 23 corresponding novel miRNAs* were discovered. Twenty-seven (36.5%) of the novel miRNAs exhibited differential QRT-PCR expression profiles in different development gibberellin-treated grapevine berries that could further confirm their existence in grapevine. QRT-PCR analysis on transcript abundance of 27 conserved miRNA family and the new candidate miRNAs revealed that most of them were differentially regulated by the gibberellin, with most conserved miRNA family and 26 miRNAs being specifically induced by gibberellin exposure. All novel sequences had not been earlier described in other plant species. In addition, 117 target genes for 29 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in gibberellin-treated grape berries. This study led to the confirmation of 101 known miRNAs and the discovery of 74 novel miRNAs in grapevine. Identification of miRNAs resulted in significant enrichment of the gibberellin of grapevine miRNAs and provided insights into miRNA regulation of genes expressed in grape berries. GSM604831 is the control for the gibberellin-treated sample.
2013-10-05 | GSE39734 | GEO
Project description:To examine the grapevine genomic methylation landscape and assess its functional significance, we generated whole genome DNA methylome maps for grapevine fruits of developmental stages. The results showed that DNA methylation happened in the grapevine fruit ripening process, and mostly happened in the biological process from the first growth stage fruit transfer to the véraison stage fruit. It further demonstrated that DNA methylation repress the gene expression. The whole-genome methylomes of grapevine fruits obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of grapevine epigenetics and the epigenetic differentiation among different fruit developmental stages.
2016-01-22 | GSE77066 | GEO
Project description:Terroir effect in the DNA methylation of grapevine
| PRJNA698897 | ENA
Project description:itis vinifera cv. Tannat is largely cultivated in Uruguay for the production of high quality red wines. Its most notable characteristic is an elevated content of polyphenolic compounds, which provide an intense purple color and remarkable antioxidant properties to the wine. To characterize the genetic components encoding this important phenotypic characteristic, the genome of the Uruguayan Tannat clone UY11 was sequenced to 134X coverage using the Illumina technology and assembled with a mixed approach of de novo assembly and iterative mapping on the PN40024 reference genome. An approach based on both reference-guided annotation and de novo transcript assembly of RNA-Seq data allowed the definition of 3,673 genes not previously annotated in PN40024 that we consider novel, and the discovery of 2,228 genes not shared with the grapevine reference genome that we consider private to Tannat. Expression analysis showed that private genes contributed substantially (more than 50%) to the overall expression of enzymes involved in phenol and polyphenol biosynthesis indicating that the dispensable portion of the grapevine genome contains many private genes which are likely to contribute to the peculiar phenotypic characteristics of this grapevine variety.
2014-01-09 | E-MTAB-4278 | biostudies-arrayexpress
Project description:Background: Global climate change, in particular the entailed predicted temperature increase, will noticeably affect plants vegetative and reproductive development. High temperatures alter the composition of the grapevine fruit, one of the most important fruits produced worldwide. This is leading to variable yield and quality, already observed in many growing regions in recent years. However, physiological processes underlying temperature response and tolerance of the grapevine fruit have hardly been investigated. Currently, all studies on fleshy fruits investigating their abiotic stress response on a molecular level were conducted during the day but possible night-specific variations were overlooked. The present study explores the grapevine fruit transcriptomic response at different developmental stages upon heat stress at day and night. Methodology/Principal Results: Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axis. The recently proposed microvine model was grown in climatic chambers in order to circumvent common constraints and biases introduced in field experiments with perennial vines. Post-véraison berry heterogeneity inside clusters was evaded upon constituting homogenous batches following organic acid and sugar measurements on individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbelGen® 090918 12X microarrays (30K). Results revealed important differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes within phenylpropanoid metabolism. Precise distinction of post-véraison stages led to a stage-specific detection of anthocyanin-related transcripts repressed by heat. Important modifications in cell wall-related processes as well as indications for a heat-induced delay of ripening and sugar accumulation were observed at véraison and reversed in later stages. Conclusion: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity to include different developmental stages and especially different time points in transcriptomic studies.
2014-01-08 | GSE53409 | GEO
Project description:Drought stress dramatically affects the growth and development of grapevine (Vitis vinifera) in many areas of the world, and identifying the mechanisms responsible for drought stress responses is therefore of great interest. The transcription factor, VlbZIP30 has been reported to enhance drought resistance in grapevine, however, the regulatory mechanisms mediated by VlbZIP30 remain poorly understood. Here, we performed chromatin immunoprecipitation (ChIP)-seq and RNA-seq analyses to identify the direct VlbZIP30 target genes at a genome-wide scale. The ChIP-seq analysis determined that VlbZIP30 binds to DNA sequences containing an ACGTG core motif, termed a G-box. By combining the ChIP-seq and RNA-seq results, we identified 48 VlbZIP30-induced target genes, related mainly to the gene ontology (GO) terms: nucleic acid-templated transcription, plant hormone and abiotic stimulus. Through ChIP-qPCR analysis, we confirmed that VlbZIP30 binds directly to the promoters of four of the target genes (VvNAC26, VvDHN1, VvGRAS17 and VvVQ6) containing a G-box motif. In addition, overexpression of VlbZIP30 led to less H2O2 accumulation compared with the wild type under drought conditions in both Arabidopsis thaliana and grapevine, indicating a role for VlbZIP30 in reactive oxygen species (ROS) scavenging. In summary, we report that VlbZIP30 promotes the activity of ROS scavenging by directly regulating the expression of downstream target genes, thereby conferring drought resistance. We also reveal that VlbZIP30 directly regulates the expression of a number of target genes (such as VvDHN1, VvGRAS17 and VvVQ6) to improve plant drought resistance.
2020-10-01 | GSE158852 | GEO
Project description:MicroRNAs (miRNAs) play a important part in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice and other plants. However, the number of miRNAs discovered in grape is relatively low and little is known about miRNAs responded gibberellin during fruit germination. In this study, a small RNA library from gibberellin grape fruits was sequenced by the high throughput sequencing technology. A total of 16,033,273 reads were obtained. 812,099 total reads representing 1726 unique sRNAs matched to known grape miRNAs. Further analysis confirmed a total of 149 conserved grapevine miRNA (Vv-miRNA) belonging to 27 Vv-miRNA families were validated, and 74 novel potential grapevine-specific miRNAs and 23 corresponding novel miRNAs* were discovered. Twenty-seven (36.5%) of the novel miRNAs exhibited differential QRT-PCR expression profiles in different development gibberellin-treated grapevine berries that could further confirm their existence in grapevine. QRT-PCR analysis on transcript abundance of 27 conserved miRNA family and the new candidate miRNAs revealed that most of them were differentially regulated by the gibberellin, with most conserved miRNA family and 26 miRNAs being specifically induced by gibberellin exposure. All novel sequences had not been earlier described in other plant species. In addition, 117 target genes for 29 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in gibberellin-treated grape berries. This study led to the confirmation of 101 known miRNAs and the discovery of 74 novel miRNAs in grapevine. Identification of miRNAs resulted in significant enrichment of the gibberellin of grapevine miRNAs and provided insights into miRNA regulation of genes expressed in grape berries. GSM604831 is the control for the gibberellin-treated sample. The mixture samples of young berries (one week after flowering) large berries (five week after flowering after flowering), and old berries (nine week after flowering) treated with gibberellin, respectively, were generated by deep sequencing, in triplicate, using Illumina 1G Genome Analyzer.
2013-10-05 | E-GEOD-39734 | biostudies-arrayexpress