Chromosome-level genome assembly of the wine grape variety 'Deckrot' and a muscat table grape cultivar G1-7720.

Govender, V.*, Rhode, C., Lashbrooke, J.

Department of Genetics, Stellenbosch University, Stellenbosch, South Africa

Grapevine (Vitis vinifera L.) is one of the most valuable perennial fruit crops cultivated worldwide for wine production and consumption as fresh fruit, raisins, and juices. The grapevine reference genome (PN40024) was the first fruit tree genome sequenced and assembled using a near-homozygous line derived from selfing of the cultivar 'Helfensteiner' and has been a major resource for studying grapevine genetics. However, grapevine breeding for traits of interest has resulted in thousands of cultivars characterised by high heterozygosity and the current reference genome does not fully represent the extensive genomic diversity among heterozygous cultivars. Recent advancements in long-read sequencing technology coupled with the decreasing cost of sequencing now make it possible to generate reference-quality genomes with high continuity for cultivars of interest. Here, we produced diploid genome assemblies of the wine grape 'Deckrot' ('Pinot gris' x 'Teinturier') and a table grape selection, G1-7720 ('Black Rose' and 'Muscat Seedless'). 'Deckrot' and G1-7720 are parents of a biparental mapping population, which shows segregation for berry aroma profiles and bunch morphology traits. Genome sequencing and assembly of the parental genomes were implemented in this study to capture all sequence variation present in this population. PacBio High-Fidelity long-read sequencing was used to produce 19 chromosomes for each haplophase for both 'Deckrot' and G1-7720. Reference-based scaffolding generated an assembly of 480.7 Mbp with an N50 scaffold length of 24.8 Mbp and a BUSCO score of 98.6% for Deckrot’s haplophase one and a 467.7 Mbp assembly with an N50 scaffold length of 24.7 Mbp and a BUSCO score of 96.9% for Deckrot’s haplophase two. For G1-7720, the two haplophase assemblies had a total scaffold length of 498.9 Mbp and 468.9 Mbp and an N50 scaffold length of 26.9 Mbp and 24.2 Mbp, respectively. Both haplophases had a BUSCO score of 98.5%. This study provides high-quality genome assemblies to investigate sequence variation underlying key grapevine breeding targets such as aromatic profiles and bunch compactness.

Keywords: grapevine, genomics, long-read sequencing, genome assembly