Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa

Abstract

Background: 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), which causes 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.

Results: We assembled and annotated a new, long-read genome assembly for 'Carlos', a cultivar of muscadine that exhibits tolerance, 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 resistance (R) genes in 'Carlos.' We further identified genes involved in Xfsf response by transcriptome sequencing 'Carlos' plants inoculated with Xfsf. We observed 234 differentially expressed genes with functions related to lipid catabolism, oxidation-reduction signaling, and abscisic acid (ABA) signaling as well as seven R genes. Leveraging public data from previous experiments of common grape inoculated with Xfsf, we determined that most differentially expressed genes in the muscadine response were not found in common grape, and three of the R genes identified as differentially expressed in muscadine do not have an ortholog in the common grape genome.

Conclusions: Our results support the utility of a pan-genome approach to identify candidate genes for traits of interest, particularly disease resistance to Xfsf, within and between muscadine and common grape.

Keywords: Grape; Muscadine grape; Pangenome; Pierce’s disease; Transcriptome.

Fig. 1

Plot of collinearity between Vitis rotundifolia‘Carlos’, V. rotundifolia ‘Trayshed’, and V. rotundifolia ‘Noble’ assemblies. The location of rDNA containing a nucleolus organizing region (NOR) is denoted by a star, while rDNA containing a 5 S array is denoted by a triangle. Symbols are correlated by color to the associated cultivar (see figure legend)

Fig. 2

Plot of collinearity betweenVitis rotundifolia‘Carlos’ andVitis viniferav2.1 assemblies. Figure generated using RIdeogram version 0.2.2. Yellow hexagons indicate the location of 35 S rDNA arrays

Fig. 3

Gene Counts of Resistance Gene Classes for Three Muscadine Cultivars and Common Grape. Gene class was assigned based on the set of domains found in the gene (Supplemental Table S7)

Fig. 4

Overlap of orthogroups associated with differentially expressed genes inVitis rotundifolia‘Carlos’ andVitis vinifera. Orthogroups contained one or more genes that were differentially expressed in the comparison. “Musc” = Muscadine Control vs. Inoculated. “Grape_CvI” = Grape Control vs. Inoculated (Wild-type). “Grape_IvK” = Grape Inoculated (Wild-type) vs. Inoculated (wzy Knockout). “Grape_CvK” = Grape Control vs. Inoculated (wzy Knockout)