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…

Technological possibilities of grape marc cell walls as wine fining agent. Effect on wine phenolic composition

Fining is a technique that is used to remove unwanted wine components that affect clarification, astringency, color, bitterness, and aroma. Fining involves the addition of adsorptive or reactive material in order to reduce or eliminate the presence of certain less desirable wine components and to ensure that a wine remains in a particular stable state for a given period of time Recently concerns have been raised about the addition of animal proteins, such as gelatin, to wine due to the disease known as bovine spongiform encephalopathy (Mad Cow disease). Although the origin of gelatins has been moved to porcine, winemakers are asking for substitute products with properties and application protocols similar to the traditional animal-derived ones, making the use of plant-derived proteins in fining a practically viable possibility. As a consequence, various fining agents derived from plants have been proposed, including proteins from cereals, legumes, and potato.

Novel approaches and promising perspectives for enhancing grapevine editing and regeneration

Grapevine (Vitis vinifera L.) is a challenging plant species to transform and regenerate due to its complex genome and biological characteristics. This limits the development of cisgenic and gene-edited varieties. One hurdle is selecting the best starting tissue for the transformation process, much like isolating suitable tissue for protoplasts. One promising method involves delivering CRISPR/Cas components to protoplasts isolated from embryogenic calli, which are then induced to regenerate. However, this process is inefficient, time-consuming, and only applicable to a few genotypes. To enhance grapevine regeneration efficiency, the expression of developmental and plant growth regulators shows promise in escaping the recalcitrance encountered in traditional tissue culture methods.

Simgi® platform as a tool for the study of wine active compounds in the  gastrointestinal tract

Simgi® platform pursues the need for dynamic in vitro simulation of the human gastrointestinal tract optimized and adapted to food safety and health fields. The platform has confirmed the model’s suitability since its first’s studies with the consistency between the simulated colonic metabolism of wine polyphenols and the metabolic evolution observed with the intake of wine in human intervention studies [1]. 

Survey assessing different practices for mechanical winter pruning in Southern France vineyards

Winter pruning is today the longest operation for hand workers in the vineyard. Over the last years, mechanical pruning practices have become popular in southern France vineyards to respond to competitiveness issue especially for the basic and mid-range wine production. Wine farmers have developed different vineyard management techniques associated with mechanical winter pruning. They sought to be precise or not to control the buds number per vine.

Impact of polyclonal selection for abiotic stress tolerance on the yield and must quality traits of grapevine varieties

The effects of climate change in viticulture are currently a major concern, with heat waves and drought affecting yield, wine quality, and in extreme cases, even plant survival. Ancient grapevine varieties have high intravarietal genetic variability that so far has been explored successfully to improve yield and must quality. Currently, there is little information available on intravarietal variability regarding responses to stress. In the current work, the intravarietal genetic variability of several Portuguese varieties was studied for yield, must quality, and tolerance to abiotic stress, through indirect, rapid, and nondestructive measurements carried out in the field.