Fig. 1: Genome assembly and core genome construction.

a Simplified illustration of the evolutionary history of the Vitis genus and the genomes included in this study. To enrich diversity in the primer design panel, interspecific hybrid grapes with diverse genetic backgrounds were sequenced. Open circle denote species represented by a sequenced hybrid accession; Closed circle denote one non-hybrid accession from this species was sequenced. Dotted lines denote more than two taxa were included in the accession. b BUSCO scores for the ten genomes examined in this study. c Synteny of the raw 10x assembly with the reference. The upper left panel is the raw pairwise genome alignment of a region on chromosome 14 constructed by minimap2; the lower right panel is filtered alignment of the same region requiring a syntenic one-to-one match. d Coverage of chromosome 2 across the nine genomes. Each line indicates a region that can be aligned to the reference.