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. 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 chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map of M. rotundifolia. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using Full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) 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 mildews. 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.…”

Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity of Vitis

“…To identify HT cases in the Vitis genomes, we used the whole-genome sequences of four Vitis species, namely, V. rotundifolia , V. arizonica , V. riparia , and V. vinifera [ 26 , 27 , 28 , 29 ]. A total of 137 plant whole-genome sequences available from the public genome sequence database ( Supplementary Table S1 ) were used to screen HTs with the Vitis genomes.…”

Evaluation of mitotic activity in tapetal cells of grapevine (Vitis L.)

“…The origin of these two different chromosome numbers in the genus, i.e., 2n=38 and 2n=40 has intrigued some researches about its origin. However, refined studies recently carried out by Cochetel et al (2021) in Muscadinia rotundifolia (n=20) [Vitis rotundifolia Michx., syn. Muscadinia rotundifolia (Michx.)…”