A telomere-to-telomere genome assembly of Vitis vinifera cv. Glera to support grapevine breeding and genetic research

Abstract

Grapevine (Vitis vinifera L.) is a clonally propagated crop of high economic value and remarkable genetic complexity, characterized by extensive structural variation and heterozygosity. These features make the generation of contiguous and accurate genome assemblies challenging, often leaving important genomic loci unresolved. Advances in sequencing technologies have enabled the generation of a high-quality telomere-to-telomere (T2T) genome references, which provide complete, gapless representations of chromosomes and allow the resolution of highly repetitive and structurally complex regions that remain inaccessible in fragmented assemblies. Here, we present a T2T genome assembly for Vitis vinifera cv. Glera, the main cultivar used for Prosecco production and one of the most economically relevant grapevine cultivars in Italy. Despite its agronomic importance and the presence of numerous clonal lines displaying phenotypic variability, genomic resources for Glera remain limited. The assembly integrates complementary sequencing technologies, combining PacBio high-fidelity (HiFi) long reads and ultra-long Oxford Nanopore Technologies (ONT) reads with chromatin conformation capture (Hi-C) data. The resulting genome provides a high-quality reference for functional genomics and breeding studies, enabling improved detection of structural variants and gene duplications, and supporting the investigation of relevant genomic regions that were previously unavailable. In a broader perspective, this work will represent a key step toward the construction of a grapevine pangenome. Using this high-quality T2T genome as a foundation, it becomes possible to move beyond single-reference frameworks and develop graph-based genomic representations capable of capturing both core and variable genomic components by integrating multiple assemblies from different cultivars. Such approaches will provide a more comprehensive view of grapevine genomic diversity and support advanced applications in population genomics, trait mapping, and genomic-assisted breeding.

Acknowledgements

This work was carried out within the framework of Glera 2.0 project promoted by Consorzio di Tutela della Denominazione di Origine Controllata Prosecco (Treviso, Italy).