A knowledge base for Vitis vinifera functional analysis

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 impr...

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Detalles Bibliográficos
Autores: Pulvirenti, Alfredo, Giugno, Rosalba, Distefano, Rosario, Pigola, Giuseppe, Mongiovi, Misael, Giudice, Girolamo, Vendramin, Vera, Lombardo, Alessandro, Cattonaro, Federica, Ferro, Alfredo
Tipo de recurso: artículo
Fecha de publicación:2015
País:España
Institución:Instituto de Salud Carlos III (ISCIII)
Repositorio:Repisalud
Idioma:inglés
OAI Identifier:oai:repisalud.isciii.es:20.500.12105/5402
Acceso en línea:http://hdl.handle.net/20.500.12105/5402
Access Level:acceso abierto
Palabra clave:EXPRESSION ANALYSIS
METABOLITE ANALYSIS
GRAPEVINE GENOME
GENE-EXPRESSION
BAC LIBRARY
SEQUENCE
IDENTIFICATION
TRANSCRIPTOME
STRESS
BERRY
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spelling A knowledge base for Vitis vinifera functional analysisPulvirenti, AlfredoGiugno, RosalbaDistefano, RosarioPigola, GiuseppeMongiovi, MisaelGiudice, GirolamoVendramin, VeraLombardo, AlessandroCattonaro, FedericaFerro, AlfredoEXPRESSION ANALYSISMETABOLITE ANALYSISGRAPEVINE GENOMEGENE-EXPRESSIONBAC LIBRARYSEQUENCEIDENTIFICATIONTRANSCRIPTOMESTRESSBERRYBackground: 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. Description: 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.BioMed Central (BMC)Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF)20172017-11-2720152015-01-0120152015-01-01journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/20.500.12105/5402reponame:Repisaludinstname:Instituto de Salud Carlos III (ISCIII)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Atribución 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repisalud.isciii.es:20.500.12105/54022026-06-12T12:43:37Z
dc.title.none.fl_str_mv A knowledge base for Vitis vinifera functional analysis
title A knowledge base for Vitis vinifera functional analysis
spellingShingle A knowledge base for Vitis vinifera functional analysis
Pulvirenti, Alfredo
EXPRESSION ANALYSIS
METABOLITE ANALYSIS
GRAPEVINE GENOME
GENE-EXPRESSION
BAC LIBRARY
SEQUENCE
IDENTIFICATION
TRANSCRIPTOME
STRESS
BERRY
title_short A knowledge base for Vitis vinifera functional analysis
title_full A knowledge base for Vitis vinifera functional analysis
title_fullStr A knowledge base for Vitis vinifera functional analysis
title_full_unstemmed A knowledge base for Vitis vinifera functional analysis
title_sort A knowledge base for Vitis vinifera functional analysis
dc.creator.none.fl_str_mv Pulvirenti, Alfredo
Giugno, Rosalba
Distefano, Rosario
Pigola, Giuseppe
Mongiovi, Misael
Giudice, Girolamo
Vendramin, Vera
Lombardo, Alessandro
Cattonaro, Federica
Ferro, Alfredo
author Pulvirenti, Alfredo
author_facet Pulvirenti, Alfredo
Giugno, Rosalba
Distefano, Rosario
Pigola, Giuseppe
Mongiovi, Misael
Giudice, Girolamo
Vendramin, Vera
Lombardo, Alessandro
Cattonaro, Federica
Ferro, Alfredo
author_role author
author2 Giugno, Rosalba
Distefano, Rosario
Pigola, Giuseppe
Mongiovi, Misael
Giudice, Girolamo
Vendramin, Vera
Lombardo, Alessandro
Cattonaro, Federica
Ferro, Alfredo
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF)
dc.subject.none.fl_str_mv EXPRESSION ANALYSIS
METABOLITE ANALYSIS
GRAPEVINE GENOME
GENE-EXPRESSION
BAC LIBRARY
SEQUENCE
IDENTIFICATION
TRANSCRIPTOME
STRESS
BERRY
topic EXPRESSION ANALYSIS
METABOLITE ANALYSIS
GRAPEVINE GENOME
GENE-EXPRESSION
BAC LIBRARY
SEQUENCE
IDENTIFICATION
TRANSCRIPTOME
STRESS
BERRY
description 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. Description: 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.
publishDate 2015
dc.date.none.fl_str_mv 2015
2015-01-01
2015
2015-01-01
2017
2017-11-27
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12105/5402
url http://hdl.handle.net/20.500.12105/5402
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Atribución 4.0 Internacional
http://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Atribución 4.0 Internacional
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BioMed Central (BMC)
publisher.none.fl_str_mv BioMed Central (BMC)
dc.source.none.fl_str_mv reponame:Repisalud
instname:Instituto de Salud Carlos III (ISCIII)
instname_str Instituto de Salud Carlos III (ISCIII)
reponame_str Repisalud
collection Repisalud
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,198674

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