title: A knowledge base for Vitis vinifera functional analysis.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Pulvirenti
authors.forename: Rosalba
authors.initials: R
authors.lastname: Giugno
authors.forename: Rosario
authors.initials: R
authors.lastname: Distefano
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Pigola
authors.forename: Misael
authors.initials: M
authors.lastname: Mongiovi
authors.forename: Girolamo
authors.initials: G
authors.lastname: Giudice
authors.forename: Vera
authors.initials: V
authors.lastname: Vendramin
authors.forename: Alessandro
authors.initials: A
authors.lastname: Lombardo
authors.forename: Federica
authors.initials: F
authors.lastname: Cattonaro
authors.forename: Alfredo
authors.initials: A
authors.lastname: Ferro
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018745:Genome, Plant / Q000235:genetics; D051188:Knowledge Bases; D035683:MicroRNAs / Q000235:genetics; D012802:Sicily; D027843:Vitis / Q000235:genetics*
chemical_list: D035683:MicroRNAs