De novotranscriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity

BMC Genomics

Research Article

Andrea Minio¹  Gianpiero Zamperin¹  Genny Buson¹  Diana Bellin¹  Alberto Ferrarini¹  Elisa Debora Zago¹  Marianna Fasoli¹  Paola Tononi¹  Sara Zenoni¹  Luca Venturini¹  Giovanni Battista Tornielli¹  Silvia Dal Santo¹  Mario Pezzotti¹  Massimo Delledonne¹ 

[1] Biotechnology Department, University of Verona, Strada Le Grazie 15, I-37134, Verona, Italy;

关键词: Transcriptomics;    RNA-Seq;    de novo;    Grape;    Varietal diversity;   

DOI  :  10.1186/1471-2164-14-41

 received in 2012-10-11, accepted in 2013-01-11,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundPlants 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.ResultsWe 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Venturini et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. 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.