Food metagenome
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PROVIDER: PRJNA289617 | ENA |
REPOSITORIES: ENA
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Project description:We applied the RNA-Seq approach to reconstruct the transcriptome of Vitis vinifera cv. Corvina, using RNA pooled from a comprehensive set of sampled tissues in different organs and development steps, and we were able to reconstruct some novel and putative private Corvina genes. We analyzed the expression of these genes in three berry developmental conditions, and posit that they may play some role in the formation of the mature organ. Background: Plants display a high genetic and phenotypic variability among different cultivars. Understanding the genetic components that contribute to phenotypic diversity is necessary to disentangle genetic factors from the environment. Given the high degree of genetic diversity among plant cultivars a whole-genome sequencing and re-annotation of each variety is required but a reliable genome assembly is hindered by the high heterozigosity and sequence divergence. Results: we show the feasibility of an approach based on sequencing of cDNA by RNA-Seq to analyze varietal diversity between a local grape cultivar Corvina and the PN40024 grape reference genome. We detected 15,260 known genes and we annotated alternative splicing isoforms for 9,463 genes. Our approach allowed to define 2,321 protein coding putative novel genes in unannotated or unassembled regions of the reference genome PN40024 and 180 putative private Corvina genes whose sequence is not shared with the reference genome. Conclusions: With a de novo assembly based approach we were able to reconstruct a substantial part of the Corvina transcriptome and we improved substantially known genes annotations by better defining the structure of known genes, annotating splicing isoforms and detecting unannotated genes. Moreover our results clearly define sets of private genes which are likely part of the âdispensableâ genome and potentially involved into influencing some cultivar-specific characteristics. In plant biology a transcriptome de novo assembly approach should not be limited to species where no reference genome is available as it can improve the annotation lead to the identification of genes peculiar of a cultivar.
2012-07-30 | E-MTAB-4220 | biostudies-arrayexpress
Project description:Grapevine is a commercially important fruit crop that provides berries for direct consumption, juice pressing, drying (raisins), and fermentation to produce wine. The economic value of the crop has encouraged many researchers to study the physiological and molecular basis of berry development, particularly processes that affect wine quality. Post-harvest withering of grapevine berries is used in the production of dessert and fortified wines to alter must quality characteristics and to increase the concentration of simple sugars. Vitis vinifera cv Corvina berries were sampled during the 2006 growing season at four developmental time points and three additional time points during the 91-day post-harvest withering process. The four developmental time points were 59, 71, 98 and 112 days after fruit set, corresponding to pre-veraison, veraison, early ripening and late ripening, and the three withering time points (WI, WII and WIII) were 35, 56 and 91 days after harvest. Three biological replicates were taken at each time point resulting in a total of 21 samples.
2010-09-24 | E-GEOD-20511 | biostudies-arrayexpress
Project description:Grape berries undergo considerable physical and biochemical changes during the ripening process. Ripening is characterized by a number of changes, including the degradation of chlorophyll, an increase in berry deformability, a rapid increase in the level of hexoses in the berry vacuole, an increase in berry volume, the catabolism of organic acids, the development of skin colour, and the formation of compounds that influence flavour, aroma, and therefore, wine quality. The aim of this work is to identify differentially expressed genes during grape ripening by microarray and real-time PCR techniques. Using a custom array of new generation, we analysed the expression of 6000 grape genes from pre-veraison to full maturity, in Vitis vinifera cultivar Muscat of Hamburg, in two different years (2006 and 2007). Five time points per year and two biological replicates per stadium were considered. To reduced intra-plant and inter-plant biological variability, for each ripening stadium we collected around hundred berries from several bunch grapes of five plants of V. vinifera cv Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.
2010-11-09 | E-MEXP-2451 | biostudies-arrayexpress
Project description:Temperature and solar radiation influence Vitis vinifera L. berry ripening. Both environmental conditions fluctuate cyclically on a daily period basis and the strength of this fluctuation affects grape ripening too. Additionally, a molecular circadian clock regulates daily cyclic expression in a large proportion of the plant transcriptome modulating multiple developmental processes in diverse plant organs and developmental phases. Circadian cycling of fruit transcriptomes has not been characterized in detail despite their putative relevance in the final composition of the fruit. Thus, in this study, gene expression throughout 24 h periods in pre-ripe berries of Tempranillo and Verdejo grapevine cultivars was followed to determine whether different ripening transcriptional programs are activated during certain times of day in different grape tissues and genotypes. Results: Microarray analyses identified oscillatory transcriptional profiles following circadian variations in the photocycle and the thermocycle. A higher number of expression oscillating transcripts were detected in samples carrying exocarp tissue including biotic stress-responsive transcripts activated around dawn. Thermotolerance-like responses and regulation of circadian clock-related genes were observed in all studied samples. Indeed, homologs of core clock genes were identified in the grapevine genome and, among them, VvREVEILLE1 (VvRVE1), showed a consistent circadian expression rhythm in every grape berry tissue analysed. Light signalling components and terpenoid biosynthetic transcripts were specifically induced during the daytime in Verdejo, a cultivar bearing white-skinned and aromatic berries, whereas transcripts involved in phenylpropanoid biosynthesis were more prominently regulated in Tempranillo, a cultivar bearing black-skinned berries. Conclusions: The transcriptome of ripening fruits varies in response to daily environmental changes, which might partially be under the control of circadian clock components. Certain cultivar and berry tissue features could rely on specific circadian oscillatory expression profiles. These findings may help to a better understanding of the progress of berry ripening in short term time scales. A total of 54 samples were hybridized. Three different circadian time course series consisted on six time point each. Series corresponded to pericarp of Verdejo grapevine cultivar and berry flesh and skin in separate of Tempranillo cultivar. Three biological replicates were analyzed for each series.
2014-03-28 | E-GEOD-52167 | biostudies-arrayexpress
Project description:Grapevine is a popular fruit crop worldwide with essential economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. To better understand this dynamic process, we applied mass spectrometry based platforms to analysis the metabolome and proteome of grape berries at 12 developmental stages covering the whole developmental process of grape berries. Primary metabolites involved in central carbon metabolism such as sugars, organic acids and amino acids metabolism together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the metabolomic and proteomic data revealed growing trajectories with minor difference indicating that grape berry development is a sequential process resulting in changes in all examined processes. The incorporation of the metabolomic and proteomic results allowed us to schematize representative metabolome and proteome candidates on sugar, glycolysis, TCA cycle, amino acid, phenylpropanoid, flavonoid biosynthetic pathways. The overview of the metabolism dynamics on both protein and metabolite level unveiled the metabolism switch and adjustments during grape berry development.
2018-10-18 | PXD003769 | Pride
Project description:Temperature and solar radiation influence Vitis vinifera L. berry ripening. Both environmental conditions fluctuate cyclically on a daily period basis and the strength of this fluctuation affects grape ripening too. Additionally, a molecular circadian clock regulates daily cyclic expression in a large proportion of the plant transcriptome modulating multiple developmental processes in diverse plant organs and developmental phases. Circadian cycling of fruit transcriptomes has not been characterized in detail despite their putative relevance in the final composition of the fruit. Thus, in this study, gene expression throughout 24 h periods in pre-ripe berries of Tempranillo and Verdejo grapevine cultivars was followed to determine whether different ripening transcriptional programs are activated during certain times of day in different grape tissues and genotypes. Results: Microarray analyses identified oscillatory transcriptional profiles following circadian variations in the photocycle and the thermocycle. A higher number of expression oscillating transcripts were detected in samples carrying exocarp tissue including biotic stress-responsive transcripts activated around dawn. Thermotolerance-like responses and regulation of circadian clock-related genes were observed in all studied samples. Indeed, homologs of core clock genes were identified in the grapevine genome and, among them, VvREVEILLE1 (VvRVE1), showed a consistent circadian expression rhythm in every grape berry tissue analysed. Light signalling components and terpenoid biosynthetic transcripts were specifically induced during the daytime in Verdejo, a cultivar bearing white-skinned and aromatic berries, whereas transcripts involved in phenylpropanoid biosynthesis were more prominently regulated in Tempranillo, a cultivar bearing black-skinned berries. Conclusions: The transcriptome of ripening fruits varies in response to daily environmental changes, which might partially be under the control of circadian clock components. Certain cultivar and berry tissue features could rely on specific circadian oscillatory expression profiles. These findings may help to a better understanding of the progress of berry ripening in short term time scales.
2014-03-28 | GSE52167 | GEO
Project description:The first genome-wide transcriptomic atlas of grapevine (Vitis vinifera) is based on 54 diverse samples expressing ~93% of predicted grapevine genes. Pollen and senescent leaves have unique transcriptomes but microarray analysis grouped all other samples into vegetative/green or mature/woody categories based on maturity rather than organ identity. This fundamental transcriptome reprograming during maturation was highlighted by three distinct statistical approaches supported by gene coexpression analysis. The shift to the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of neighboring genes and global regulation based on codon preference. A total of 54 grapevine samples, covering most of the Grape organs at different stages, were collected. Three biological replicates were taken for each sample, resulting in a total of 162 observations. The collected plant organs were: bud, inflorescence, tendril, leaf, stem, root, developing berry, withering berry, seed, rachis, anther, carpel, petal, pollen, and seedling.
2012-09-10 | E-GEOD-36128 | biostudies-arrayexpress
Project description:Grape berry development is a highly coordinated, intricate and complex process with many morphological, biochemical and physiological changes occurring during the ripening process. Equally, ripening is an organoleptic characteristic linked to fruit development. The fruits Seedless (FS) and Victoria (VT) grape varieties exhibit many morphological and phytochemical differences, but genetic mechanisms underlying them remain poorly explored. Herein, we comparatively analysed the phenotypic and transcriptomic patterns of Victoria (VT) and Flame Seedless (FS) grape varieties during berry development. We studied the physiological analysis and transcriptomic profiles sequencing were performed at four berry developmental stages time-points (40, 50, 60 and 80 DPA). Notably, the VT variety berry size was comparatively larger to the FS variety. At maturity, 80DPA, the FS soluble solids were 61.8% higher than VT. Further, a total of 4889 and 2802 DEG’s were identified from VT and FS 40 DPA to 80 DPA development stages, respectively. 1386 DEGs were common in the two varieties. GO analysis identified Cysteine biosynthetic process, response to red light, chlorophyll binding, polysaccharide biosynthetic process and chloroplast thylakoid membrane as some of the dominant terms under the biological processes, molecular function and cellular component categories.
2023-07-01 | GSE153998 | GEO