A complete gene expression atlas of Vitis vinifera cv. Corvina: a useful guide to the grapevine transcriptome

This thesis describes a complete gene expression atlas of the common grapevine (Vitis vinifera), which is the most widely-cultivated fruit crop in the world. New insights into the transcriptional complexity during berry development were firstly provided using RNA-Seq technology. The setting up of NimbleGen platform enabled the launch of the challenging project of the grapevine gene expression map. The first genome-wide transcriptomic atlas of grapevine is based on 54 diverse samples expressing ~93% of predicted grapevine genes. Pollen and senescent leaves have unique transcriptomes but microarray analysis grouped all other samples into vegetative/green or ripe/woody categories based on maturity rather than organ identity. This fundamental transcriptome reprogramming during maturation was highlighted by three distinct statistical approaches (Pearson’s correlation distance, O2PLS-DA and topic-model-based biclustering analyses) supported by gene coexpression analysis. The shift to the ripe/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of neighbouring genes and global regulation based on codon preference.