Genomics of Grapevine Diseases

Grapevines are susceptible to a broad variety of diseases caused by necrotrophic and biotrophic fungal pathogens that greatly impact grape production worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the mechanisms of pathogenicity of grapevine pathogens. In particular, the characterization of the structure, function and evolutionary dynamics of virulence factors can help guiding and prioritizing breeding efforts. To identify virulence genes of economically relevant grapevine fungal pathogens, we apply a combination of genomic approaches, including whole-genome shotgun sequencing, multiple isolate re-sequencing, transcriptional profiling, comparative genomics, and virulence-factor focused annotation. Recently, we released the draft genome sequences of pathogens associated with three major trunk diseases of grapevine: Esca (Tognina minima), Botryosphaeria dieback (Neofusicoccum parvum), and Eutypa dieback (Eutypa lata). Transcriptome profiling during growth on axenic media and during plant infections strengthened our virulence factor annotation, as well as provided insights in the transcriptional regulation of the potential virulence factors. The identification of virulence factors and understanding of their functions from a single pathogen genome provide a static and limited view of the pathogen diversity and evolution. We have thus expanded the whole-genome sequencing to multiple isolates of E. lata and N. parvum with varying aggressiveness that were collected from distinct geographical locations and plant hosts.