GSE116274
Whole-transcriptome RNA-seq analysis of grapevine-Botrytis cinerea interaction during latent infection of berries (“noble rot”)
Purpose: High throughput sequencing technologies provide a unique opportunity to deeply investigate the molecular mechanisms involved in plant-pathogen interaction. Botrytis cinerea, is the agent of grapevine grey mould, but in yet uncharacterized environmental conditions, a latent infection can occur determining favourable metabolic and physico-chemical berry modifications which possibly contribute to the typical aromas of “passito” wines (“noble rot”). The present project aims at the identification of the genes deployed by B. cinerea during grape berries colonization in the latent form, in comparison with the saprophytic growth in vitro. Methods: A total of 300 healthy berries have been artificially inoculated one by one with B. cinerea by injecting conidia under berry skin, in controlled conditions, reproducing the pourri plein stage of noble rot. Control samples (300 berries) have been inoculated with water. The saprophytic growth was obtained in liquid nutrient medium in laboratory flasks, and the mycelium collected by filtration. The RNA-sequencing experiments on healthy or infected samples in biological triplicate resulted in 27 data sets to be analyzed (Illumina NextSeq500 paired-end sequencing; 533.779.730 total reads, 150 Gb of data). Conclusions: This work identified important molecular mechanisms involved in Botrytis cinerea colonization of grapevine berries during the noble rot infection. Overall design: mRNA profiles of Garganega berries infected with Botrytis cinerea (noble rot) were either compared to mRNA profiles of uninfected Garganega berries (control berries) or  to those of Botrytis cinerea grown in vitro (saprophytic growth). All mRNA profiles were generated by deep sequencing, in triplicate, using Illumina NextSeq500.