A comprehensive isoform catalogue to investigate transcriptional responses to water stress in grapevine

Abstract

Climate change is increasing the frequency and duration of droughts, leading to water deficits strongly affecting grapevine berry and wine quality. Alternative splicing mechanism allows the production of multiple isoforms from a single gene.

Therefore, it plays a role in adjusting gene regulation in response to abiotic stresses, drought in particular. However, isoform-level resources remain limited for Vitis vinifera.

Our project aimed to: (1) build a comprehensive catalogue of isoforms expressed in grapevine across tissues, cultivars and conditions, and (2) identify genes showing isoform-level changes under drought stress conditions.

We generated an extensive reference using PacBio Iso-Seq data complemented by public datasets. The dataset spans five tissues and twelve cultivars, including leaf and berry samples exposed to drought stress for 9 cultivars. Adedicated annotation workflow identified 23,411 genes with a median of four transcripts per gene, providing a high-resolution view of isoform diversity across tissues, cultivars and conditions. With this new resource, we identified that around 70% of the multi-exonic genes of Vitis vinifera undergo alternative splicing.

Expression of genes and isoforms was quantified from short-read RNA-seq of berries and leaves grown under contrasting drought stress conditions. This analysis highlighted splicing events affecting genes associated with drought responses.

The resulting isoform catalogue constitutes a unique reference for the grapevine community and supports future work on the molecular mechanisms underlying adaptation and cultivar specific response at the isoform level in grapevine. In addition, the isoform catalogue will be accessible to the community through VitExpress expression atlas platform to allow public consultation of the expressed isoforms.