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…

Influence of harvest time and withering length combination on reinforced Nebbiolo wines: phenolic composition, colour traits, and sensory profile

Sforzato di Valtellina DOCG is a reinforced dry red wine produced in the mountain area of Valtellina alpine valley (North Italy), using ‘Nebbiolo’ grapes that undergo a withering process. This process impacts on the grape composition due to a sugar concentration and changes in secondary metabolism influencing volatile organic compounds (VOCs) and polyphenols.

Q-NMR measurements: quantitative analysis of wine composition applied to Bordeaux red wines authenticity control

Traceability of wine is today a consumer demand and a scientific challenge. The methods of analysis must be able to control three fundamental parameters: the geographical origin, the grape varieties, and the vintage.

Practical Aspects of Viticultural Zoning In South Africa

Depuis 1973, une commission statutaire administre la législation qui régit le zonage vitivinicole en Afrique du Sud. La province «Le Cap de l’ouest» cerne toutes les zones viticoles sauf quatre unités. Pour la plupart, le Cap de l’ouest a un climat méditerranéen. Les zones viticoles – qui produisent les «vins d’origine» – sont des régions, des districts, des quartiers et des domaines. Les régions sont vastes, séparées par la topographie, par ex. des chaînes de montagnes et des fleuves. Généralement, chaque région représente une zone climatique. Le climat de chaque district est plus homogène. Les quartiers sont exactement délimités par le climat, la topographie et la géologie. Les domaines sont les plus petits. Chaque domaine doit avoir un seul propriétaire.

Oak wood seasoning: impact on oak wood chemical composition and sensory quality of wine

Oak wood selection and maturation are essential steps in the course of barrel fabrication. Given the existence of many factors involved in the choice of raw material and in natural seasoning of oak wood, it is very difficult to determine the real impact of seasoning and selection factors on oak wood composition. A sampling was done to study the evolution of oak wood chemical composition during four seasoning steps: non matured, 12 months, 18 months and 24 months. For this sampling, three selection factors were taken into account: age, grain type and the Polyphenolic Index measured by Oakscan®. Besides extractables
(~10%), three polymers constitute the main part of oak wood: cellulose, hemicelluloses and lignins.

Efficiency of alternative chemical and physical treatments in reducing Brettanomyces Bruxellensis from oak wood

Oak barrels form an integral part of wine production, especially that of high quality wines. However, due to its porosity, wood presents an ecological niche for microbial proliferation and is highly susceptible to microbial spoilage which could cause considerable economic losses. Brettanomyces bruxellensis, the most commonly encountered microorganism responsible for spoilage during barrel ageing, can remain in barrels after barrel sanitation to contaminate new batches of wine after refilling. Therefore, effective sanitation treatments are of utmost importance to prevent recurring wine spoilage.