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…

Effects of the biodynamic preparations 500 and 501 on vine and berry physiology, pedology and the soil microbiome

In the pursuit of increasing sustainability, climate change resiliency and independence of synthetic pesticides in agriculture, the interest of consumers and producers in organic and biodynamic farming is steadily increasing. This is in particular the case for the vitivinicultural industry in Europe, where more and more producers are converting from organic to biodynamic farming. However, clear scientific evidence showing that biodynamic farming improves vine physiology, vine stress resilience, berry or wine quality, or is more sustainable for the environment is still lacking although this issue has been addressed by several research teams worldwide.

Analysis of climate spatio-temporal variability in the Conegliano-Valdobbiadene DOCG wine district

Local climate characterization is fundamental in terroir description, yet global change perspectives raise questions about its feasibility, since temporal stability cannot be no more assumed for the forthcoming years.

Phenotyping bud break and trafficking of dormant buds from grafted vine

In grapevine, phenology from bud break to berry maturation, depends on temperature and water availability. Increases in average temperatures accelerates initiation of bud break, exposing newly formed shoots to detrimental environmental stresses. It is therefore essential to identify genotypes that could delay phenology in order to adapt to the environment. The use of different rootstocks has been applied to change scion’s characteristics, to adapt and resist to abiotic and biotic stresses[1].

Wine tourism as a catalyst for sustainable competitive advantage: unraveling the role of winery image and reputation

This study examines the impact of wine tourism development on the sustainable competitive advantage of Spanish wineries, while also exploring the mediating roles of winery image and winery reputation in this relationship.

REVINE project : regenerative agricultural approaches to improve ecosystem services in Mediterranean vineyards

REVINE is a 3 year European projected funded by PRIMA programme which proposes the adoption of regenerative agriculture practices with an innovative and original perspective, in order to improve the resilience of vineyards to climate change in the Mediterranean area.
Regenerative agriculture ameliorates soil structure and microbial biodiversity that, in turn, leads to crop resilience against biotic and abiotic stressful factors. Moreover, enrichment of beneficial microbes in the rhizosphere, such as PGPR and PGPF, are known to trigger the plant immunity inducing the priming state.