Unknown,Transcriptomics,Genomics,Proteomics

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Vitis vinifera strain:Corvina Transcriptome or Gene expression

ABSTRACT: We applied the RNA-Seq approach to reconstruct the transcriptome of Vitis vinifera cv. Corvina, using RNA pooled from a comprehensive set of sampled tissues in different organs and development steps, and we were able to reconstruct some novel and putative private Corvina genes. We analyzed the expression of these genes in three berry developmental conditions, and posit that they may play some role in the formation of the mature organ. Background: Plants display a high genetic and phenotypic variability among different cultivars. Understanding the genetic components that contribute to phenotypic diversity is necessary to disentangle genetic factors from the environment. Given the high degree of genetic diversity among plant cultivars a whole-genome sequencing and re-annotation of each variety is required but a reliable genome assembly is hindered by the high heterozigosity and sequence divergence. Results: we show the feasibility of an approach based on sequencing of cDNA by RNA-Seq to analyze varietal diversity between a local grape cultivar Corvina and the PN40024 grape reference genome. We detected 15,260 known genes and we annotated alternative splicing isoforms for 9,463 genes. Our approach allowed to define 2,321 protein coding putative novel genes in unannotated or unassembled regions of the reference genome PN40024 and 180 putative private Corvina genes whose sequence is not shared with the reference genome. Conclusions: With a de novo assembly based approach we were able to reconstruct a substantial part of the Corvina transcriptome and we improved substantially known genes annotations by better defining the structure of known genes, annotating splicing isoforms and detecting unannotated genes. Moreover our results clearly define sets of private genes which are likely part of the âdispensableâ genome and potentially involved into influencing some cultivar-specific characteristics. In plant biology a transcriptome de novo assembly approach should not be limited to species where no reference genome is available as it can improve the annotation lead to the identification of genes peculiar of a cultivar.

INSTRUMENT(S): Illumina HiSeq 1000

ORGANISM(S): Vitis vinifera

SUBMITTER: Luca Venturini

PROVIDER: E-MTAB-4220 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Venturini Luca L Ferrarini Alberto A Zenoni Sara S Tornielli Giovanni Battista GB Fasoli Marianna M Dal Santo Silvia S Minio Andrea A Buson Genny G Tononi Paola P Zago Elisa Debora ED Zamperin Gianpiero G Bellin Diana D Pezzotti Mario M Delledonne Massimo M

BMC genomics 20130118

<h4>Background</h4>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.<h4>Results</h4>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 k ...[more]

PMID: 23331995

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Dataset Information

Vitis vinifera strain:Corvina Transcriptome or Gene expression

Publications

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

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