Diploid chromosome-scale assembly of the<i>Muscadinia rotundifolia</i>genome supports chromosome fusion and disease resistance gene expansion during<i>Vitis</i>and<i>Muscadinia</i>divergence

Abstract Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in southeastern United States. M. rotundifolia is resistant to many of pathogens that detrimentally affect Vitis vinifera, grape species commonly used winemaking. For this reason, a valuable genetic resource breeding. Single-molecule real-time reads were combined with optical maps reconstruct two haplotypes each 20 cv. Trayshed chromosomes. The completeness and accuracy assembly confirmed using high-density linkage map. Protein-coding genes annotated an integrated comprehensive approach. This included full-length cDNA sequencing (Iso-Seq) improve gene structure hypothetical spliced variant predictions. Our data strongly support chromosomes 7 are fused pinpoint location fusion Cabernet Sauvignon PN40024 chromosome 7. Disease-related numbers similar, but their clustering locations different. A dramatic expansion Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on 12 at Resistance Uncinula necator 1 (RUN1)/Resistance Plasmopara viticola (RPV1) locus, which confers strong dominant resistance powdery downy mildews. genome browser, annotation, Blast tool available www.grapegenomics.com.