terclim by ICS banner
IVES 9 IVES Conference Series 9 Haplotype-resolved genome assemblies of Chasselas and Ugni Blanc

Haplotype-resolved genome assemblies of Chasselas and Ugni Blanc

Abstract

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous real-field genetic pool Vitis vinifera cultivars by combining high-fidelity long-read sequencing (HiFi) and highthroughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar. The deletions/insertions, inversions, translocations, and duplications provide insight into the evolutionary history and parental relationship among grape varieties. Integration of de novo single long-read sequencing of full-length transcript isoforms (Iso-Seq) yielded a highly improved genome annotation. Given its higher contiguity, and the robustness of the IsoSeq-based annotation, the Chasselas assembly meets the standard to become the annotated reference genome for Vitis vinifera.

DOI:

Publication date: July 6, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Guillaume Madignier1,2, Anis Djari1, Olivia Di Valentin1, Thibault Gillet1, Pierre Frasse1, Amel Djouhri1, Guojian Hu1,2, Sebastien Julliard3, Mingchun Liu4, Yang Zhang4, Farid Regad1, Julien Pirrello1, Elie Maza1,*, and Mondher Bouzayen1,*

1Laboratoire de Recherche en Sciences Végétales–Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan 31326, France
2Fondation Jean Poupelain, Cognac, Javrezac 16100, France
3Conservatoire du vignoble charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
4Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China

Contact the author*

Keywords

Genome assembly, Genome annotation, HiFi, Hi-C, Iso-Seq.

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Effectiveness of carboxymethyl cellulose (CMC) on tartaric stabilization of cava base wine

Recent EU regulations allow the use of carboxymethylcellulose (CMC) as a stabilization agent in wine. We tested CMC in bases for sparkling wines, which must be stabilized before the second fermentation that raises alcohol concentration by 1,5%.

Changes in the composition and extractability of flavonoids in Cabernet-Sauvignon: influence of site, climate and vine water status

The purpose of the study was to monitor berry development as a function of site, vine water status and climate in order to improve our understanding of the role played by climate change on secondary metabolites relevant to wine quality.

Landscape study of the Suzette rural district. A vineyard in the heart of the Dentelles de Montmirail

Le territoire de Suzette se développe sur un grand coteau viticole et boisé situé au cœur du site naturel des Dentelles de Montmirail (40km au nord d’Avignon). Ce site est à la fois l’un des pôles d’attraction touristique du département et le lieu d’une production viticole renommée (Gigondas, Vacqueyras, Beaumes de Venise, … ). Cet ensemble remarquable de terrasses viticoles et de crêtes rocheuses et boisées, forme un des paysages emblématiques du Vaucluse. La commune est actuellement soumise à une importante pression foncière due à une forte demande résidentielle. Le paysage du coteau forme et possède de ce fait un patrimoine culturel de valeur et une image de marque importante pour la production viticole locale.

Managing precision irrigation in vineyards: hydraulic and molecular signaling in eight grapevine varieties

Understanding the physiological and molecular bases of grapevine responses to mild to moderate water deficits is fundamental to optimize vineyard irrigation management and identify the most suitable varieties. In Mediterranean regions, the higher frequency of heat waves and droughts highlights the importance of precision irrigation to meet vine water demands and demonstrates the necessity for a deeper understanding of the different physiological responses among varieties under water stress. In this context, previous reports show an interplay between stomatal regulation of transpiration and changes in leaf hydraulic conductivity, also with the involvement of aquaporins (AQPs), particularly under water stress. However, how those signaling mechanisms are regulated in different grapevine varieties along phenological phases is unclear.

Application of DEXI PM Vigne sustainability tool to the assessment of alternative vineyard protection strategies

Implementing alternative grapevine systems that incorporate sustainable strategies and innovative farming practices is essential. However, we lack tools for measuring the impact of these new practices on the overall sustainability of vineyards. DEXi PM Vigne (Gary et al., 2015) is a tool developed for ex ante assessment of the sustainability of grapevine cropping systems, from the plot to the farm scale. In the present study, we focused on implementing new strategies of integrated crop protection management with limited pesticide use in vineyards.