Assembling the diversity: reconstruction and characterization of ecotypes’ proprietary set of genes by RNA-Seq
Luca Venturini, Alberto Ferrarini, Andrea Minio, Genny Buson, Sara Zenoni, Mario Pezzotti, Marianna Fasoli, Massimo Delledonne
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
I’ll present the results obtained by the application of this strategy to Vitis vinifera cv Corvina in order to characterize its proprietary set of genes.
