Supporting data for "The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired"

Unlike most other grapevine varieties, teinturier varieties produce berries with pigmented flesh due to anthocyanin production within the flesh. As a result, teinturier varieties are of interest not only for their ability to enhance the pigmentation of wine blends but also for their health benefits. They also serve as valuable systems for investigating anthocyanin production in plants. Here, we assembled and annotated the Dakapo and Rubired genomes, two teinturier varieties. For Dakapo, we used a combination of Nanopore sequencing, Illumina sequencing, and scaffolding to the existing grapevine genome assembly to generate a final assembly of 508.5 Mbp. A combination approach of <i>de novo</i> annotation and lifting over annotations from the existing grapevine reference genome resulted in the annotation of 36,940 genes in the Dakapo assembly. For Rubired, PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long. <i>De novo</i> annotation of the diploid Rubired genome yielded annotations for 56,681 genes across both haplotypes and unplaced contigs. The genomes for both varieties are highly contiguous (scaffold N50 &gt; 24.9 Mbp) and highly complete (BUSCO &gt; 97.7%). The Dakapo and Rubired genome assemblies and annotations will provide genetic resources for future investigations into berry flesh pigmentation and other traits of interest in grapevine.