Beyond the Grape Genome: Construction of a Vineyard Metagenome Reference

Biotic interactions in the vineyard contribute to define grape productivity. Many microorganisms, including viruses, bacteria and fungi are capable of infecting grapevines causing important damage if left uncontrolled. Many more microorganisms, endophytic or epiphytic, are not pathogenic and may play a positive role in wine grape yield and chemical composition. Here, I will discuss the use of different whole genome sequencing approaches to develop a multi-species genome reference for grapevines and their most commonly associated micro-organisms to study their interactions under natural field settings. Single molecule real time sequencing (SMRT) technology was used to generate high-quality genome references for grape and some of the most economically important grape pathogens, including Eutypa lata, Neofusicoccum parvum, Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. Highly contiguous genomes were obtained and a combination of ab initio and evidence based methods were used to annotate their protein-coding genes. I will provide an update on the sequencing efforts of Cabernet Sauvignon and other common wine grape varieties. De novo assembly of short reads provided rapid access to the genomes of other fungi often associated with grapevines, including Phaeomoniella chlamydospora, Erysiphe necator, Diplodia seriata, Botryosphaeria dothidea, and several Lasiodiplodia and Neofusicoccum species.  The availability of annotated genomes for grape and the most relevant grape-associated microorganism has allowed us to construct a multi-species reference for mapping and quantifying DNA and RNA sequencing reads. I will describe how an optimized bioinformatics approach has been used to produce quantitative assessments of species composition as well as genome-wide transcriptional profiling of plant and microbiome gene expression in the vineyard.