Ontology highlight
ABSTRACT:
PROVIDER: PRJNA799026 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17681690_1.fastq.gz | Fastqsanger.gz | |||
| SRR17681690_2.fastq.gz | Fastqsanger.gz | |||
| SRR17681691_1.fastq.gz | Fastqsanger.gz | |||
| SRR17681691_2.fastq.gz | Fastqsanger.gz | |||
| SRR17681692_1.fastq.gz | Fastqsanger.gz |
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Project description:Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susceptibility among grapevine varieties suggest the existence of specific genetic features associated with resistance to the phytoplasma and/or possibly with its vector. In this work, RNA-Seq was used to compare early transcriptional changes occurring during the three-trophic interaction between the phytoplasma, its vector and the grapevine, represented by two different cultivars, one very susceptible to the disease and the other scarcely susceptible. Background: Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susceptibility among grapevine varieties suggest the existence of specific genetic features associated with resistance to the phytoplasma and/or possibly with its vector. In this work, RNA-Seq was used to compare early transcriptional changes occurring during the three-trophic interaction between the phytoplasma, its vector and the grapevine, represented by two different cultivars, one very susceptible to the disease and the other scarcely susceptible. The comparison of the transcriptomic responses highlighted both passive and active defense mechanisms against the vector and/or the pathogen in the scarcely-susceptible variety, as well as the capacity of the phytoplasmas to repress the defense reaction against the insect in the susceptible variety.
2019-06-13 | E-MTAB-7710 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high throughput sequencing technologies has enabled the revelation of novel miRNAs. Although there are two recent reports on high throughput sequencing analysis of small RNA libraries from different organs of two grapevine wine varieties, there were significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. Here, we initially constructed a small RNA library of flower and fruit tissues of a table grapevine cultivar ‘Summer Black’ and performed sequencing and analysis of sRNAs using the Illumina Solexa platform, expecting to discover more miRNAs related to the development of grapevine flowers and berries and the formation of dessert quality in grapevine berries. Totally, 130 conserved grapevine miRNA (Vv-miRNA) belonging to 28 Vv-miRNA families were validated, and 92 novel potential grapevine-specific ones representing 80 unique ones were first discovered. Forty-two (48.84%) of the novel miRNAs possessed differential semi-quantitative PCR expression profiles in various grapevine tissues that could further confirm their existence in the grapevine, among which twenty were expressed only in grapevine berries, indicating some fruit-specificity. 130 target genes for 46 novel miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed.
2013-10-05 | GSE24531 | GEO
Project description:MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high throughput sequencing technologies has enabled the revelation of novel miRNAs. Although there are two recent reports on high throughput sequencing analysis of small RNA libraries from different organs of two grapevine wine varieties, there were significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. Here, we initially constructed a small RNA library of flower and fruit tissues of a table grapevine cultivar M-bM-^@M-^XSummer BlackM-bM-^@M-^Y and performed sequencing and analysis of sRNAs using the Illumina Solexa platform, expecting to discover more miRNAs related to the development of grapevine flowers and berries and the formation of dessert quality in grapevine berries. Totally, 130 conserved grapevine miRNA (Vv-miRNA) belonging to 28 Vv-miRNA families were validated, and 92 novel potential grapevine-specific ones representing 80 unique ones were first discovered. Forty-two (48.84%) of the novel miRNAs possessed differential semi-quantitative PCR expression profiles in various grapevine tissues that could further confirm their existence in the grapevine, among which twenty were expressed only in grapevine berries, indicating some fruit-specificity. 130 target genes for 46 novel miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The resultant 35nt sequence data were filtered according to base quality value. The remained sequences were used to trim 5' and 3' adaptors. The clean tags were used for further analysis.
2013-10-05 | E-GEOD-24531 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to detect the environmental influence on small RNAs population (miRNAs and other smallRNAs) in berries from two different grapevine varieties, evaluating Genotype x Environment interactions. Methods: The grapevine berries were collected in liquid nitrogen and their small RNA fractions were isolated from total RNA for library construction and subsequent sequencing on an Illumina HiSeq 2000. Results: Reads were mapped to the reference Vitis vinifera L. genomic sequence V1 (PN40024, (Jaillon et al., 2007) using Bowtie and retaining reads perfectly aligned to the genome. The static clustering analysis was carried out, using a proximity-based pipeline built with custom Perl and database scripts and MySQL database queries, to group and quantify clusters of small RNAs. The identification of annotated (conserved or known) and novel (or specie-specific) miRNAs was carried out applying a conservative and robust pipeline. Conclusions: Our results show that the distribution of small RNA-producing loci is variable between the two cultivars, and that the level of variation depends on the vineyard. Differently, the profile of miRNA accumulation mainly depends on the developmental stage. One of the environment, Riccione, maximizes the differences between the varieties, promoting the production of more than one thousand specific small RNA loci and modulating their expression depending on the cultivar and the maturation stage. The grapevine berries were collected for the sequencing at four different developmental stages from Cabernet Sauvignon (CS) and Sangiovese (SG) clones grown side by side in three different vineyards. The vineyards are located in three typical wine making italian areas: Bolgheri (Bol), a coastal area of Tuscany, Montalcino (Mont) a mountain area of Tuscany, and Riccione (Ric), a plain area of Emilia-Romagna.
2016-08-16 | E-GEOD-85611 | biostudies-arrayexpress
Project description:We report the berry pericarp transcriptomic profiles of 5 red Vitis vinifera varieties: Sangiovese, Barbera, Negro amaro, Refosco and Primitivo at 4 growth stages: pea-sized berries (Bbch 75) at almost 20 days after flowering, berries beginning to touch (Bbch77) just prior véraison, the softening of the berries (Bbch 85) at the end of véraison and berries ripe for harvest (Bbch 89) mRNA profiles of 5 red grapevine varieties at 4 growth stages were generated by deep sequencing, in triplicate, using Illumina Hiseq 1000.
2015-01-19 | E-GEOD-62744 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to detect the environmental influence on small RNAs population (miRNAs and other smallRNAs) in berries from two different grapevine varieties, evaluating Genotype x Environment interactions. Methods: The grapevine berries were collected in liquid nitrogen and their small RNA fractions were isolated from total RNA for library construction and subsequent sequencing on an Illumina HiSeq 2000. Results: Reads were mapped to the reference Vitis vinifera L. genomic sequence V1 (PN40024, (Jaillon et al., 2007) using Bowtie and retaining reads perfectly aligned to the genome. The static clustering analysis was carried out, using a proximity-based pipeline built with custom Perl and database scripts and MySQL database queries, to group and quantify clusters of small RNAs. The identification of annotated (conserved or known) and novel (or specie-specific) miRNAs was carried out applying a conservative and robust pipeline. Conclusions: Our results show that the distribution of small RNA-producing loci is variable between the two cultivars, and that the level of variation depends on the vineyard. Differently, the profile of miRNA accumulation mainly depends on the developmental stage. One of the environment, Riccione, maximizes the differences between the varieties, promoting the production of more than one thousand specific small RNA loci and modulating their expression depending on the cultivar and the maturation stage.
2016-08-16 | GSE85611 | GEO
Project description:A dissection of Genotype x Environment interactions in grapevine berry using a multi-layered -omics approach Grapevine, the most widely-cultivated perennial fruit crop, is also considered a very environmentally sensitive crop. It is characterized by remarkable phenotypic plasticity which in turn is believed to effectively buffer environmental extremes especially through transcriptomic and epigenomic reprogramming. Thus, the final phenotype (P) of a given vine is the result of the close interaction between its genetic composition (G) and the environment (E). Here we analyzed Genotype x Environment (GxE) interactions in two grapevine varieties by characterizing their transcriptome plasticity when cultivated in different environments. Specifically, two genotypes (Sangiovese and Cabernet Sauvignon) were cultivated in three different locations in Italy (Bolgheri -littoral Tuscany-, Montalcino – Appennine Tuscany- and Romagna -foothill area-), trained in an almost identical manner, and sampled at four developmental stages over two grapevine growing seasons, 2011 and 2012, for a total of 144 samples that were analyzed by hybridization to a whole-genome microarray and by Reduced Representation Bisulfite Sequencing (RRBS-seq). In order to study the relationships among differential gene expression profiles and environmental cues, we have developed a new statistical data mining tool based on data reduction approaches which allowed a dissection of the transcriptomic data into stage-specific, cultivar-related and GxE important clusters of gene expression. This deep inspection of inner relationships between the different dataset variables allowed the identification of several candidate genes that could represent putative markers of berry quality traits in grapevine GxE interactions. Moreover, the methods used to establish our model provide a framework for the analysis of transcriptome plasticity in other crops as they respond to diverse environments.
2018-04-09 | GSE98762 | GEO
Project description:Arbuscular mycorrhizal symbiosis improves water and nutrient uptake by plants and provides them other ecosystem services. Grapevine is one of the major crops in the world. V. vinifera scions are generally grafted onto a variety of rootstocks that confer different levels of resistance against different pests, tolerance to environmental stress, and influence the physiology of the scions. Arbuscular mycorrhizal fungi are involved in the root architecture and in the immune response to soil-borne pathogens. However, the fine-tuned regulation and the transcriptomic plasticity of rootstocks in response to mycorrhization are still unknown. We compared the responses of 10 different grapevine rootstocks to arbuscular mycorrhizal symbiosis (AMS) formed with Rhizophagus irregularis DAOM197198 using RNA sequencing-based transcriptome profiling. We have highlighted a few shared regulation mechanisms, but also specific rootstock responses to R. irregularis colonization. A set of 353 genes was regulated by AMS in all ten rootstocks. We also compared the expression level of this set of genes to more than 2,000 transcriptome profiles from various grapevine varieties and tissues to identify a class of transcripts related to mycorrhizal associations in these 10 rootstocks. Then, we compared the response of the 351 genes upregulated by mycorrhiza in grapevine to their Medicago truncatula homologs in response to mycorrhizal colonization based on available transcriptomic studies. More than 97% of these homologs were expressed in at least one transcriptome profile, and 64% in all profiles. At the intra-specific level, we described for the first time shared and specific grapevine rootstock genes in response to R. irregularis symbiosis. At the inter-specific level, we defined a shared subset of mycorrhiza-responsive genes
2023-06-10 | GSE234583 | GEO
Project description:Plants have great potential to protect against pathogens and other abiotic stress, and thus the interaction between signaling networks of defense is incredible. This can be activated and express with the application of growth elicitors and antimicrobial natural compounds. In the present study we used natural polysaccharide, Chitosan (15kDa) against Grey mold in two grape varieties (Shine-muscat and Kyoho). The finding depicted that the interaction of DEG and KEGG in control and treated samples of grapevine, which provides the evidence for selection of gray mold related defense genes and chitosan for subsequent grapevine production/postharvest programs.
2020-12-31 | GSE129046 | GEO