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…

Ageing of sweet wines: oxygen evolution according to bung and barrel type

Barrel ageing is a crucial step in the wine process because it allows many changes to the wine as enrichment, colour stabilization, clarification and also a slow oxygenation. Effects of the oak barrel have to be known to prevent oxidation of the wine. The type of bung used during ageing is also a parameter to consider. Ageing sweet wines in barrel is a real challenge. These wines may need some oxygen at the beginning of ageing but they should be protected at the end of their maturation, to avoid oxidation.

Aspects concernant les relations entre quelques composantes de la biomasse viticole, en fonction de l’offre des ressources écologiques

Ecological resources represent vegetation factors, or even production factors, in quantitative expression. These, used by plants, transformed and organized according to their genetic program, become the material components of biomass. Subsequently, the ecological resources can be used as synthetic indicators of the ecological supply, necessary for the analysis of favorability for the understanding of ecosystems.

Evolución de los compuestos fenólicos durante el envero y la maduración en la DO Tarragona

La evolución de los contenidos en las pieles de compuestos fenólicos (fenólicos totales, antocianos totales, antocianos individuales por HPLC, catequinas y proantocianidoles) a lo largo

The influence of RNAi-expressing rootstocks in controlling grey mold on grapevine cultivars

Worldwide, with an average of 6.7 million cultivated hectares, of which exclusively 51% in Europe (faostat, 2021), the production of table and wine grapes is a leading sector, with continued growth in Europe in the area devoted to vine cultivation. during the growing season, most of the plant organs can be susceptible to several fungal and oomycete diseases, leading to important economic losses and causing detrimental effects on fruit quality. the increasingly scarce availability of fungicidal products, often also related to their relative impact on the environment, coupled with the emergence of resistance in the pathogen to these products, make defence increasingly challenging.

Spatial variability of grape berry maturation program at the molecular level 

The application of sensors in viticulture is a fast and efficient method to monitor grapevine vegetative, yield and quality parameters and determine their spatial intra-vineyard variability. Molecular analysis at the gene expression level can further contribute to the understanding of the observed variability by elucidating how pathways responsible for different grape quality traits behave in zones diverging for one or the other parameter. The intra-vineyard variability of a Cabernet Sauvignon vineyard was evaluated by a standard Normalized Difference Vegetation Index (NDVI) mapping approach, employing UAV platform, accompanied by detailed ground-truthing (e.g. vegetative, yield, and berry ripening compositional parameters) that was applied in 14 spots in the vineyard. Berries from different spots were additionally investigated by microarray gene expression analysis, performed at five time points from fruit set to full ripening.