Corvina fungal metataxonomics
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: MTBLS392
PROVIDER: PRJEB14642 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1593563.fastq.gz | Fastqsanger.gz | |||
| ERR1593564.fastq.gz | Fastqsanger.gz | |||
| ERR1593565.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:<p>The composition and changes of the fungal population and of the metabolites present in grapes and in ferments of Vitis vinifera L. cv. Corvina, one of the major components of the Amarone musts, were dissected aiming at the identification of constant characteristics possibly influenced by the productive process. The fungal populations and metabolomic profiles were analyzed in three different vintages. 454-pyrosequencing on the ribosomal ITS1 region has been used to identify the fungal population present in Corvina grapes and fresh must. Samples were also subjected to metabolomics analysis measuring both free volatile compounds and glycosylated aroma precursors through an untargeted approach with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. Albeit strongly dependent on the climate, both the mycobiota and metabolome of Corvina grapes and fresh musts show some characteristics recursive in different vintages. Such persistent characteristics are likely determined by the method adopted to produce Amarone or other dry wines made from partially dried grapes. In particular, the harsh conditions imposed by the prolonged withering appear to contribute to the shaping of the fungal populations. The fungal genera and metabolites present in different vintages in V. vinifera L. cv. Corvina grapes and fresh musts represent core components of the peculiar technique of production of Amarone. Their identification allows the in-depth understanding and improved control of the process of production of this economically and culturally relevant wine.</p><p><br></p><p><strong>Linked cross omic data sets:</strong></p><p>Meta-taxonomics data associated with this study are available in the European Nucleotide Archive (ENA): accession number <a href='https://www.ebi.ac.uk/ena/browser/view/PRJEB15229' rel='noopener noreferrer' target='_blank'>PRJEB15229</a>.</p>
2017-11-14 | MTBLS392 | MetaboLights
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:Vitis vinifera strain:Corvina Transcriptome or Gene expression
| PRJNA169607 | ENA
Project description:Protein expression from berry skin of four different red grape biotypes was compared at a proteome-wide level by bottom-up shotgun proteomics, label free quantification and MaxQuant-assisted computational analysis. Red grapes were from a purebred Vitis vinifera (Aglianico cv.), a V. vinifera (local Sciascinoso cv.) grafted onto an American rootstock, an interspecific hybrid (V. vinifera × V. labrusca, Isabel) and an uncharacterized red grape with some hybrid lineage, as demonstrated by the presence of relatively high amounts of anthocyanidin 3,5-O-diglucosides. The aim was assessing the differences among red grape biotypes at a protein expression levels, also addressing the possible effect of the grafting on the phenotypic expression of some key metabolic enzymes in grape berries.
2022-02-22 | PXD025784 | Pride
Project description:Amplicon-based metagenomics analysis of Vitis vinifera L. cv. Corvina grapes and fresh musts
| PRJEB15229 | ENA
Project description:We determined the RNA sequence of V. vinifera cv. Victoria and V. vinifera cv. Muscat Hamburg grapes to reveal the transcriptomics variations between summer and winter berries under a double cropping system. Transcriptomics analysis showed that the upregulated VviDXSs, VviPSYs, and VviCCDs expressions might contribute to accumulations of terpenes or norisoprenoids in winter berries.
2021-03-13 | GSE168785 | GEO
Project description:Methods:transcriptomes of the different development stages of Vitis vinifera cv. Cabernet Sauvignon and Vitis quinquangularis accession Danfeng-2 were analyzed using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed: TopHat followed by Cufflinks. mRNA profiles of different development stages of Vitis vinifera cv. Cabernet Sauvignon and Vitis quinquangularis accession Danfeng-2 were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.
2015-12-23 | E-GEOD-76256 | biostudies-arrayexpress
Project description:Methods:transcriptomes of the different development stages of Vitis vinifera cv. Cabernet Sauvignon and Vitis quinquangularis accession Danfeng-2 were analyzed using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed: TopHat followed by Cufflinks.
2015-12-23 | GSE76256 | GEO