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De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity

BACKGROUND: Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to disentangle genetic and environmental factors. RESULTS: We have shown that cDNA se...

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Autores principales: Venturini, Luca, Ferrarini, Alberto, Zenoni, Sara, Tornielli, Giovanni Battista, Fasoli, Marianna, Santo, Silvia Dal, Minio, Andrea, Buson, Genny, Tononi, Paola, Zago, Elisa Debora, Zamperin, Gianpiero, Bellin, Diana, Pezzotti, Mario, Delledonne, Massimo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556335/
https://www.ncbi.nlm.nih.gov/pubmed/23331995
http://dx.doi.org/10.1186/1471-2164-14-41
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author Venturini, Luca
Ferrarini, Alberto
Zenoni, Sara
Tornielli, Giovanni Battista
Fasoli, Marianna
Santo, Silvia Dal
Minio, Andrea
Buson, Genny
Tononi, Paola
Zago, Elisa Debora
Zamperin, Gianpiero
Bellin, Diana
Pezzotti, Mario
Delledonne, Massimo
author_facet Venturini, Luca
Ferrarini, Alberto
Zenoni, Sara
Tornielli, Giovanni Battista
Fasoli, Marianna
Santo, Silvia Dal
Minio, Andrea
Buson, Genny
Tononi, Paola
Zago, Elisa Debora
Zamperin, Gianpiero
Bellin, Diana
Pezzotti, Mario
Delledonne, Massimo
author_sort Venturini, Luca
collection PubMed
description BACKGROUND: Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to disentangle genetic and environmental factors. RESULTS: We have shown that cDNA sequencing by RNA-seq is a robust approach for the characterization of varietal diversity between a local grapevine cultivar (Corvina) and the PN40024 reference genome. We detected 15,161 known genes including 9463 with novel splice isoforms, and identified 2321 potentially novel protein-coding genes in non-annotated or unassembled regions of the reference genome. We also discovered 180 apparent private genes in the Corvina genome which were missing from the reference genome. CONCLUSIONS: The de novo assembly approach allowed a substantial amount of the Corvina transcriptome to be reconstructed, improving known gene annotations by robustly defining gene structures, annotating splice isoforms and detecting genes without annotations. The private genes we discovered are likely to be nonessential but could influence certain cultivar-specific characteristics. Therefore, the application of de novo transcriptome assembly should not be restricted to species lacking a reference genome because it can also improve existing reference genome annotations and identify novel, cultivar-specific genes.
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spelling pubmed-35563352013-01-30 De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity Venturini, Luca Ferrarini, Alberto Zenoni, Sara Tornielli, Giovanni Battista Fasoli, Marianna Santo, Silvia Dal Minio, Andrea Buson, Genny Tononi, Paola Zago, Elisa Debora Zamperin, Gianpiero Bellin, Diana Pezzotti, Mario Delledonne, Massimo BMC Genomics Research Article BACKGROUND: Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to disentangle genetic and environmental factors. RESULTS: We have shown that cDNA sequencing by RNA-seq is a robust approach for the characterization of varietal diversity between a local grapevine cultivar (Corvina) and the PN40024 reference genome. We detected 15,161 known genes including 9463 with novel splice isoforms, and identified 2321 potentially novel protein-coding genes in non-annotated or unassembled regions of the reference genome. We also discovered 180 apparent private genes in the Corvina genome which were missing from the reference genome. CONCLUSIONS: The de novo assembly approach allowed a substantial amount of the Corvina transcriptome to be reconstructed, improving known gene annotations by robustly defining gene structures, annotating splice isoforms and detecting genes without annotations. The private genes we discovered are likely to be nonessential but could influence certain cultivar-specific characteristics. Therefore, the application of de novo transcriptome assembly should not be restricted to species lacking a reference genome because it can also improve existing reference genome annotations and identify novel, cultivar-specific genes. BioMed Central 2013-01-18 /pmc/articles/PMC3556335/ /pubmed/23331995 http://dx.doi.org/10.1186/1471-2164-14-41 Text en Copyright ©2013 Venturini et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Venturini, Luca
Ferrarini, Alberto
Zenoni, Sara
Tornielli, Giovanni Battista
Fasoli, Marianna
Santo, Silvia Dal
Minio, Andrea
Buson, Genny
Tononi, Paola
Zago, Elisa Debora
Zamperin, Gianpiero
Bellin, Diana
Pezzotti, Mario
Delledonne, Massimo
De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity
title De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity
title_full De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity
title_fullStr De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity
title_full_unstemmed De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity
title_short De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity
title_sort de novo transcriptome characterization of vitis vinifera cv. corvina unveils varietal diversity
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556335/
https://www.ncbi.nlm.nih.gov/pubmed/23331995
http://dx.doi.org/10.1186/1471-2164-14-41
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