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 high‐throughput 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.

Download the abstract

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…

Insight on Lugana flavor with a new LC-MS method for the detection of polyfunctional thiols

The analysis of polyfunctional thiols in wine is challenging due to their low abundance and instability within a complex matrix. However, volatile thiols are highly aroma-active, making their accurate quantification in wine at low concentrations crucial [1].

Read More

Viticultural landscape: history of a challenging coexistence between grapevines and humans 

Vitis vinifera is the most grown grapevine species, which originated about 6 million years ago in the trans-caucasian area as the ancestral (wild) type v. Vinifera spp. Sylvestris. On the other hand, the human being (homo sapiens) is much younger since he originated about 300.000 years ago in north africa.

Read More

Diffuse light due to wildfire smoke enhances gas exchange of shaded leaves

The risk of wildfires is increasing as the frequency and severity of drought and heat waves continue to rise. Wildfires are associated with the combustion of plant materials and emit smoke. In the atmosphere, smoke may spread readily across large areas. Smoke is composed of solid and liquid phase particulates and gases and has been identified as a causal agent of “smoke taint” in wine. On a smoky day, the intensity of direct light decreases because these particulates scatter sunlight. Even though this effect is frequently assumed to decrease plant photosynthesis, this assumption ignores the potential changes in diffuse light and may be based on scant evidence.

Read More

Sviluppo di una metodologia di tracciabilità e definizione dell’impronta petrochimica in suoli e vini della Sicilia occidentale nella piana di Marsala (TP)

I risultati delle ricerche condotte in un vigneto sperimentale di Marsala (TP), scelto per omogeneità di fattori bio-agronomici (età, tecniche colturali, potenzialità vegetativa e produttiva)

Read More

Different soil types and relief influence the quality of Merlot grapes in a relatively small area in the Vipava Valley (Slovenia) in relation to the vine water status

Besides location and microclimatic conditions, soil plays an important role in the quality of grapes and wine. Soil properties influence…

Read More