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…

Impact of drought stress on concentration and composition of wine proteins in Riesling

Protein haze in white wines is a major technological and economic problem of the wine industry. Field tests were carried out in steep slope vineyards planted with Riesling grapes over 3 dry growing seasons to study the effect of drought stress on the concentration of proteins in the resulting wines. Plots suffering from drought stress were compared with surrounding drip irrigated plots. Riesling grapes were processed into wines by conventional procedures. Protein amounts of the isolated wine colloids of the stressed samples were always higher than those of the watered samples(mean watered 13.8 ± 0.44, mean stressed 17.4 ± 0.40 g 100 g-1). As a consequence, higher bentonite doses were needed to achieve protein haze stability of the drought stressed treatments.

Reconstructing ancient microbial fermentation genomes from the wine residues of Herod, Roman king of Judea

The fortress of the Herodium, built towards the end of the first century BCE/ante Cristo, on the orders of Herod the Great, Roman client king of Judea, attests the expansion of Roman influence in the eastern Mediterranean. During archaeological excavations of the Herodium in 2017[1], a winery was discovered on the ground floor of the palace, with an assortment of clay vessels in situ, including large dolia – clay fermentation vessels each capable of fermenting up to 300-400 L of wine. Thanks to the recent progresses in the field of paleogenomics[2], we could analyse the organic material consistent with grape pomace at the bottom of these vessels, by extracting and sequencing the DNA using shotgun metagenomics and targeted capture, aiming for enrichment of DNA from fermentation associated microbes.

Selecting varieties best adapted to current and future climate conditions based on ripening traits

Aim: The aim of this study was to quantify key berry sugar accumulation traits and characterize their plasticity in response to climate variation from data collected from different cultivars over seven years from an experimental vineyard.

Release and perception of γ-nonalactone and massoia lactone in the red wine matrix: impact of ethanol and acidity

Climate change (CC) is altering grape/wine composition, leading to challenges in maintaining wine sensory quality.

Volatile organic compounds: a role in elicitor-induced resistance of grapevine against pathogens?

As Vitis vinifera varieties are susceptible to fungal diseases, numerous chemical treatments are generally required to ensure the quantity and quality of the harvest. However, in the context of sustainable viticulture, there are increasing societal request, political incitation, and winegrowers’ awareness to reduce the use of pesticides.