Dataset Information

A knowledge base for Vitis vinifera functional analysis.

ABSTRACT: Vitis vinifera (Grapevine) is the most important fruit species in the modern world. Wine and table grapes sales contribute significantly to the economy of major wine producing countries. The most relevant goals in wine production concern quality and safety. In order to significantly improve the achievement of these objectives and to gain biological knowledge about cultivars, a genomic approach is the most reliable strategy. The recent grapevine genome sequencing offers the opportunity to study the potential roles of genes and microRNAs in fruit maturation and other physiological and pathological processes. Although several systems allowing the analysis of plant genomes have been reported, none of them has been designed specifically for the functional analysis of grapevine genomes of cultivars under environmental stress in connection with microRNA data.Here we introduce a novel knowledge base, called BIOWINE, designed for the functional analysis of Vitis vinifera genomes of cultivars present in Sicily. The system allows the analysis of RNA-seq experiments of two different cultivars, namely Nero d'Avola and Nerello Mascalese. Samples were taken under different climatic conditions of phenological phases, diseases, and geographic locations. The BIOWINE web interface is equipped with data analysis modules for grapevine genomes. In particular users may analyze the current genome assembly together with the RNA-seq data through a customized version of GBrowse. The web interface allows users to perform gene set enrichment by exploiting third-party databases.BIOWINE is a knowledge base implementing a set of bioinformatics tools for the analysis of grapevine genomes. The system aims to increase our understanding of the grapevine varieties and species of Sicilian products focusing on adaptability to different climatic conditions, phenological phases, diseases, and geographic locations.

SUBMITTER: Pulvirenti A

PROVIDER: S-EPMC4464603 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A knowledge base for Vitis vinifera functional analysis.

Pulvirenti Alfredo A Giugno Rosalba R Distefano Rosario R Pigola Giuseppe G Mongiovi Misael M Giudice Girolamo G Vendramin Vera V Lombardo Alessandro A Cattonaro Federica F Ferro Alfredo A

BMC systems biology 20150601

<h4>Background</h4>Vitis vinifera (Grapevine) is the most important fruit species in the modern world. Wine and table grapes sales contribute significantly to the economy of major wine producing countries. The most relevant goals in wine production concern quality and safety. In order to significantly improve the achievement of these objectives and to gain biological knowledge about cultivars, a genomic approach is the most reliable strategy. The recent grapevine genome sequencing offers the opp ...[more]

PMID: 26050794

Similar Datasets

Project description:Grape is one of the most important fruit crops worldwide. The suitable geographical locations and productivity of grapes are largely limited by temperature. Vitis amurensis is a wild grapevine species with remarkable cold-tolerance, exceeding that of Vitis vinifera, the dominant cultivated species of grapevine. However, the molecular mechanisms that contribute to the enhanced freezing tolerance of V. amurensis remain unknown. Here we used deep sequencing data from restriction endonuclease-generated cDNA fragments to evaluate the whole genome wide modification of transcriptome of V. amurensis under cold treatment. Vitis vinifera cv. Muscat of Hamburg was used as control to help investigate the distinctive features of V. amruensis in responding to cold stress. Approximately 9 million tags were sequenced from non-cold treatment (NCT) and cold treatment (CT) cDNA libraries in each species of grapevine sampled from shoot apices. Alignment of tags into V. vinifera cv. Pinot noir (PN40024) annotated genome identified over 15,000 transcripts in each library in V. amruensis and more than 16,000 in Muscat of Hamburg. Comparative analysis between NCT and CT libraries indicate that V. amurensis has fewer differential expressed genes (DEGs, 1314 transcripts) than Muscat of Hamburg (2307 transcripts) when exposed to cold stress. Common DEGs (408 transcripts) suggest that some genes provide fundamental roles during cold stress in grapes. The most robust DEGs (more than 20-fold change) also demonstrated significant differences between two kinds of grapevine, indicating that cold stress may trigger species specific pathways in V. amurensis. Functional categories of DEGs indicated that the proportion of up-regulated transcripts related to metabolism, transport, signal transduction and transcription were more abundant in V. amurensis. Several highly expressed transcripts that were found uniquely accumulated in V. amurensis are discussed in detail. This subset of unique candidate transcripts may contribute to the excellent cold-hardiness of V. amurensis.

Project description:The health status of the native grapevine Vitis vinifera subsp. sylvestris (Gmeli) Hegi in natural areas in Europe has received little attention. A survey was carried out on wild grapevines in Tuscany (Italy), where isolates of the Grapevine rupestris stem pitting virus (GRSPaV), Grapevine leafroll-associated virus 1 and 3 (GLRaV-1 and GLRaV-3) and Grapevine virus A (GVA) were detected. The complete coat protein (CP) region of these isolates was sequenced to investigate the relationship of the viral variants from Tuscan wild grapevines with isolates from different geographical origins. According to the phylogenetic analyses, GLRaV-1 and GLRaV-3 isolates from Tuscan wild grapevines clustered with isolates from cultivated grapevines with nucleotide sequence identities ranging from 66% to 87% and from 72.5% to 99% respectively, without any correlation between the distribution and geographical origin. Conversely, GRSPaV and GVA isolates clustered together with other Italian isolates from V. vinifera with nucleotide sequence identities ranging from 71.14% to 96.12% and from 73.5% to 92%, respectively. Our analysis of the whole amino acid sequences revealed a high conservation level for the studied proteins explained by a selective pressure on this genomic region, probably due to functional constraints imposed on CP, such as specific interactions with cellular receptors in the insect vectors necessary for successful transmission. In addition, analyses of genetic recombination suggest no significant point mutations that might play a significant role in genetic diversification. The dN/dS ratio also estimated a low number of non-silent mutations, highlighting the purifying selective pressure. The widespread distribution of the Rugose wood complex (GRSPaV and GVA associated disease) in comparison with the Grapevine Leafroll associated viruses (GLRaV-1 and -3) could explain the major geographical correlation found for the viral variants detected in Tuscany.

Dataset Information

A knowledge base for Vitis vinifera functional analysis.

Publications

A knowledge base for Vitis vinifera functional analysis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets