Vitis rotundifolia cultivar:Carlos Genome sequencing

Muscadine grape (Vitis rotundifolia) is resistant to many of the pathogens that negatively impact the production of common grape (V. vinifera), including the bacterial pathogen Xylella fastidiosa, subsp. Fastidiosa (Xfsf), commonly known as Pierce's Disease (PD). Previous studies in common grape have indicated Xfsf delays host immune response with a complex O-chain antigen produced by the wzy gene. Muscadine cultivars range from tolerant to completely resistant to Xfsf, but the mechanism is unknown. We performed transcriptome sequencing to characterize the response of 'Carlos', a cultivar of muscadine that exhibits tolerance, to inoculation with Xfsf. We assembled and annotated a new, long-read genome assembly for 'Carlos' to build upon the existing genetic resources available for muscadine. We used these resources to construct an initial pan-genome for three cultivars of muscadine and one cultivar of common grape. This pan-genome contains a total of 34,970 synteny-constrained entries containing genes of similar structure. Comparison of resistance gene content between the 'Carlos' and common grape genomes indicates an expansion of R genes in 'Carlos.' Based on transcriptome data, we observed 234 differentially expressed genes in response to Xfsf inoculation in 'Carlos'. Leveraging data from previous experiments of common grape inoculated with PD, we determined that most differentially expressed genes in the muscadine response were not found in common grape. Minimal overlap of the genes associated with Xfsf response were observed between grape species. These results indicate a unique response to Xfsf in muscadine that bypasses the O-chain antigen.