Unknown,Transcriptomics,Genomics,Proteomics

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Vitis vinifera Transcriptome or Gene expression

ABSTRACT: itis vinifera cv. Tannat is largely cultivated in Uruguay for the production of high quality red wines. Its most notable characteristic is an elevated content of polyphenolic compounds, which provide an intense purple color and remarkable antioxidant properties to the wine. To characterize the genetic components encoding this important phenotypic characteristic, the genome of the Uruguayan Tannat clone UY11 was sequenced to 134X coverage using the Illumina technology and assembled with a mixed approach of de novo assembly and iterative mapping on the PN40024 reference genome. An approach based on both reference-guided annotation and de novo transcript assembly of RNA-Seq data allowed the definition of 3,673 genes not previously annotated in PN40024 that we consider novel, and the discovery of 2,228 genes not shared with the grapevine reference genome that we consider private to Tannat. Expression analysis showed that private genes contributed substantially (more than 50%) to the overall expression of enzymes involved in phenol and polyphenol biosynthesis indicating that the dispensable portion of the grapevine genome contains many private genes which are likely to contribute to the peculiar phenotypic characteristics of this grapevine variety.

INSTRUMENT(S): Illumina HiSeq 1000

ORGANISM(S): Vitis vinifera

SUBMITTER: Massimo Delledonne

PROVIDER: E-MTAB-4278 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description: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.

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Vitis vinifera Transcriptome or Gene expression

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