The great phenotypic diversity between plant varieties is a manifestation of a major variation at the genetic level, which so far has been largely described as differences relative to a specific reference genome and its annotation. The natural diversity cannot be entirely captured by this approach, as many ecotypes feature quite divergent loci and possess genes which are not shared with the rest of the species – a situation described accurately by the term pan-genome. A well-thought RNA-Seq experiment on a variety can dodge these problems altogether by reconstructing the whole transcriptome, leading to a clear view of the single-base differences as well as to the detection of peculiar genes and isoforms We applied this strategy to Vitis vinifera cv Corvina in order to characterize its genetic diversity by discovery its proprietary set of genes. Initially we sequenced pooled cDNAs isolated from 45 different conditions and organs, leading to the identification of 45 sequences specific of our variety which are enriched on vacuole transport and cell wall modulation.
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