ABSTRACT
Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking throughout Europe and in New World wine regions. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed (Trayshed, henceforth) chromosomes. Completeness and accuracy of the assembly was confirmed using a high-density linkage map of M. rotundifolia. Protein-coding genes were annotated using an integrated comprehensive approach that included full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data confirmed the fusion of chromosomes 7 and 20, which reduced the number of chromosomes in Vitis versus Muscadinia and pinpointed the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. The numbers of nucleotide binding site leucine-rich repeats (NBS-LRR) in Trayshed and Cabernet Sauvignon were similar, but their locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like-X (TIR-X) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/ Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildew. A genome browser for Trayshed, its annotation, and an associated Blast tool are available at www.grapegenomics.com.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Reference numbers for data available in public repositories:
- NCBI: PRJNA635946 and PRJNA593045
- Zenodo DOI: 10.5281/zenodo.3866087