Diploid chromosome-scale assembly of theMuscadinia rotundifoliagenome supports chromosome fusion and disease resistance gene expansion duringVitisandMuscadiniadivergence

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.

Rootstock influences the effect of grapevine leafroll‐associated viruses on berry development and metabolism via abscisic acid signalling

“…NBS‐LRR genes confer resistance to powdery and downy mildew in grapevine (Riaz et al, 2011; Zini et al, 2019). The abundance of these genes varies among Vitis species and are particularly dense at resistance loci (Cochetel et al, 2021). The HR to viruses is mediated by resistance (R) genes.…”

Rootstocks influence the response of ripening grape berries to leafroll associated viruses

“…NBS-LRR genes confer resistance to powdery and downy mildew in grapevine (Riaz et al ., 2011; Zini et al ., 2019). The abundance of these genes varies among Vitis species and are particularly dense at resistance loci (Cochetel et al ., 2021). Hypersensitive response (HR) to viruses is mediated by R genes.…”

Haplotype-resolved powdery mildew resistance loci reveal the impact of heterozygous structural variation on NLR genes inMuscadinia rotundifolia

“…The haplotypes of Trayshed's R loci, Run1.2 and Run2.2, were differentiated to determine the effect of NLR composition on PM resistance. The boundaries of Run1.2 were assigned by aligning the primer sequences of Run1.2-associated SSR markers to both haplotypes on M. rotundifolia Trayshed chromosome 12 (Cochetel et al, 2021) 1. This indicates that haplotype switching occurred during Trayshed assembly and phasing.…”

“…The first diploid chromosome-scale genome assembly of a muscadine grape was recently published and represents a valuable resource for characterizing the genetic basis of other PM resistance loci in M. rotundifolia (Cochetel et al, 2021). A first analysis of the Run1.2 locus suggested an expansion of TIR-NBS-LRR genes in M. rotundifolia Trayshed relative to Cabernet Sauvignon (Cochetel et al, 2021).…”