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…

Leaf necrosis induced by the insecticide carbaryl in Vitis rupestris ‘B38’

Carbaryl is an acetylcholine esterase inhibitor-type insecticide used for pest control on grapevine. We repeatedly observed the occurrence of interveinal leaf necrosis following carbaryl spray application in a Vitis rupestris x Vitis riparia F1 hybrid progeny vineyard. Spray applications induced necrosis in this progeny under both Missouri and New York field conditions an approximate one-to-one sensitive-to-insensitive segregation ratio and with 42% concordance. Results of subsequent in vitro experiments established causality between carbaryl treatment and leaf necrosis and confirmed the pattern of segregation observed in the field. We consistently map this phenotype to a major QTL on chromosome 16 of the female parent V. rupestris ‘B38’ regardless of whether we used field or in vitro-generated phenotype data.

The entomopathogenic fungus Metarhizium robertsii and its endophytic potential in grapevine to regulate radicicole grape phylloxera populations

Grape phylloxera (GP) (Daktulosphaira vitifoliae Fitch, 1855) devastated European vineyards in the 19th century by attacking Vitis vinifera roots. Today, grafting onto resistant American rootstocks remains its primary control strategy, but GP continues to threaten non-grafted vineyards, prompting the search for alternative control solutions.

Oak wood influence on the organoleptic perception of red wine

Some wood substances such as ellagitannins (vescalagin, castalagin, grandinin, roburins (A, B, C, D, E)…) can be extracted during wine ageing in oak barrels. The level of these hydrolysable tannins in wine depends of the species and origin of oak wood as well as its treatment during barrel realization.

Estimating grapevine water status: a combined analysis of hyperspectral image and 3d point clouds

Mild to moderate and timely water deficit is desirable in grape production to optimize fruit quality for winemaking. It is crucial to develop robust and rapid approaches to assess grapevine water stress for scheduling deficit irrigation. Hyperspectral imaging (HSI) has the potential to detect changes in leaf water status, but the robustness and accuracy are restricted in field applications.

Techniques for sunburn reduction in bunches in Vitis vinifera L. cv. Graciano

Sunburn results from a combination of excessive photosynthetically active radiation (PAR) and UV radiation and temperature that can be exacerbated by other stress factors such as water deficit. Sunburn is a physiological disorder that affects the visual and organoleptic properties of grapes. The appearance of brown and necrotic spots severely affects the commercial value of the fruit, and in extreme cases, significantly decreases yield. This damage occurs with some frequency in sensitive varieties such as Graciano.