Ontology highlight
ABSTRACT:
PROVIDER: PRJNA615210 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11424163.fastq.gz | Fastqsanger.gz | |||
| SRR11424164.fastq.gz | Fastqsanger.gz | |||
| SRR11424165.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome profiling by RNA sequencing determined the genome-wide patterns of expression of N. parvum virulence factors when PDA or grape wood were provided as nutrient source and during an extensive interaction time course with grapevine stem.
2017-03-08 | GSE85079 | GEO
Project description:Flavonoid biosynthesis in grape berry skin is affected by environmental factors such as light and temperature. However, the components of the light-signaling and low-temperature-induced ABA signaling networks related to flavonoid accumulation in grape berry skin have not been fully elucidated. To clarify details of the possible light- and ABA-related signal transduction networks, we performed comprehensive transcriptome analysis using grape berries cultured under different light and temperature conditions. We identified 40 light-inducible genes, 55 low-temperature-inducible genes, and 34 genes induced by light plus low temperature.
2014-12-16 | GSE64153 | GEO
Project description:We conducted transcript profiling and metabolome profiling induced by UV irradiation in grape berry skin. Transcriptome analysis was carried out with genome-wide microarray and two hundred thirty eight genes were more than 5-fold up-regulated by UV irradiation. The enrichment analysis showed GO terms including stilbene synthase (STS) gene. Moreover, the principal component analysis (PCA) of metabolome analysis showed a compound, identified resveratrol, accumulated in grape berry skin specifically. Our result clearly shows that UV irradiation induced only accumulation of resveratrol and its analogues but did not induce accumulation of the other phenolic compounds.
2014-12-01 | GSE59436 | GEO
Project description:Grape skin transcriptome to reveal genes related with resveratrol accumulation
2020-07-20 | E-CURD-39 | ExpressionAtlas
Project description:Light environments have long been known to influence grape (Vitis vinifera L.) berry development and biosynthesis of phenolic compounds, and ultimately affect wine quality. Here, the accumulation and compositional changes of hydroxycinnamic acids (HCAs) and flavonoids, as well as global gene expression were analyzed in Cabernet Sauvignon grape berries under sunlight exposure treatments at different phenological stages. Sunlight exposure did not consistently affect the accumulation of berry skin flavan-3-ol or anthocyanin among different seasons due to climatic variations, but increased HCA content significantly at véraison and harvest, and enhanced flavonol accumulation dramatically with its timing and severity degree trend. As in sunlight exposed berries, a highly significant correlation was observed between the expression of genes coding phenylalanine ammonia-lyase, 4-coumarate: CoA ligase, flavanone 3-hydroxylase and flavonol synthase family members and corresponding metabolite accumulation in the phenolic biosynthesis pathway, which may positively or negatively be regulated by MYB, bHLH, WRKY, AP2/EREBP, C2C2, NAC, and C2H2 transcription factors (TFs). Furthermore, some candidate genes required for auxin, ethylene and abscisic acid signal transductions were also identified which are probably involved in berry development and flavonoid biosynthesis in response to enhanced sunlight irradiation. Taken together, this study provides a valuable overview of the light-induced phenolic metabolism and transcriptome changes, especially the dynamic responses of TFs and signaling components of phytohormones, and contributes to the further understanding of sunlight-responsive phenolic biosynthesis regulation in grape berries.
2020-09-02 | GSE157347 | GEO
Project description:Basal leaf removal has been widely practiced to increase cluster sunlight exposure, control berry rot and eventually improve grape berry quality. Early leaf removal performed in cool region appeared to benefit the accumulation of norisoprenoids and monoterpenes. However, effects of this canopy management and leaf moving on volatile profiles and transcriptome of grape berry in warm region characterized with strong sunshine and arid climate were paid less attention. To cope with multiple possible effects caused by global warming, researches in warm region are urgently needed to provide a guide for adjusting the sunlight exposure treatment to adapt the climate change.In Manas county of Xinjiang province, sunlight exposure treatments performed in this study resulted in decreased β-carotene and lutein, which mainly responsible for the reduced norisoprenoids in ripening grapes. Substrate competition due to the up-regulation of VvTPS-a and VvNCED3 may contribute to the decreased concentration of monoterpenes in exposed berries. The notable increased C6 alcohols in the grape berries treated by leaf removal applied at veraison (LR-V), was mainly attribute to the enhanced substrate availability of linoleic acid and linolenic acid together with the higher expression of VvLOXO and VvADH1. Free C6 aldehyde was reduced by half leaf removal applied at veraison (HLR-V), leaf moving at veraison (LM-V) and leaf removal applied at berry pepper-corn size (LR-PS). Moreover, transcriptomic analysis indicated that both LR-V and LM-V treated grape berry implemented multiple stress-mitigation strategies to acclimate the improved sunlight exposure. Interestingly, photosynthesis-related genes in grape berry were primarily up-regulated by LR-V as a consequence of carbohydrate source removal rather than improved sunlight exposure. Weighted gene co-expression network analysis (WGCNA) suggested that the genes encoding malate synthase and 3-oxoacyl-(acyl carrier protein) reductase show a significant correlation with the accumulation of C6 alcohol.
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Project description:Grape skin transcriptome to reveal genes related with resveratrol accumulation
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Project description:Nutrient-starvation induced lipid accumulation has been reported in diverse algae, including diatoms. Molecular mechanisms underlying lipid accumulation in nutrient-starved algae are of interest to inform genetic engineering strategies aimed at improving lipid productivity. Diatom cell walls are made of nanostructured silica which is a unique feature of the group and silicon deprivation induces both growth arrest and lipid accumulation. In this work, we report the whole cell transcript level response during silicon starvation induced lipid accumulation.
2015-12-31 | GSE75651 | GEO
Project description:Light conditions significantly influence grape berry ripening and the accumulation of phenolic compounds, but the underlying molecular basis remains partially understood. Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes. Bagging treatments had limited effects on berry quality attributes at harvest and did not consistently affect phenolic acid biosynthesis between seasons. Significantly elevated flavan-3-ol and flavonol contents were detected in re-exposed berries after bagging during early-developmental stages, while bagging after véraison markedly inhibited skin anthocyanin accumulation. Several anthocyanin derivatives and flavonol glycosides were identified as marker phenolic metabolites for distinguishing bagged and non-bagged grapes. Coordinated transcriptional changes in the light signaling components CRY2 and HY5/HYHs, transcription regulator MYBA1, and enzymes LAR, ANR, UFGT and FLS4, coincided well with light-responsive biosynthesis of the corresponding flavonoids. The activation of multiple hormone signaling pathways after both light exclusion and re-exposure treatments was inconsistent with the changes in phenolic accumulation, indicating a limited role of plant hormones in mediating light/darkness-regulated phenolic biosynthesis processes. Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes. Altogether, our findings provide novel insights into the understanding of berry phenolic biosynthesis under light/darkness and practical guidance for improving grape features.
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Project description:Nutrient-starvation induced lipid accumulation has been reported in diverse algae, including diatoms. Molecular mechanisms underlying lipid accumulation in nutrient-starved algae are of interest to inform genetic engineering strategies aimed at improving lipid productivity. Diatom cell walls are made of nanostructured silica which is a unique feature of the group and silicon deprivation induces both growth arrest and lipid accumulation. In this work, we report the whole cell transcript level response during silicon starvation induced lipid accumulation. Analyzed mRNA from cells after 0, 4, 8, 12, 18, and 24 hr of silicon starvation using the Affymetrix GeneChip whole genome tiling array. Initial analysis of gene level expression was performed using the Affymetrix Expression Console Software, version 1.1. No biological replicates were performed. 0 hr is used as a reference point.
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