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…

How sensor technologies combined with artificial intelligence increase the efficiency in grapevine breeding (research): current developments and future perspectives

Viticulture and grapevine breeding programs have to face and adapt to the rapidly changing growing conditions due to the ongoing climate change, the scarcity of resources and the demand for sustainability within the whole value chain of wine production. In times of highly effective and cost-efficient genotyping technologies routinely applied in plant research and breeding, the need for comparable high-speed and high-resolution phenotyping tools has increased substantially. The disciplines of grapevine research, breeding and precision viticulture picked up this demand – mostly independent from each other – by the development, validation and establishment of different sensor technologies in order to extend management strategies or to transform labor-intensive and expensive phenotyping.

Improving shelf life of viticulture-relevant biocontrol and biostimulant microbes using CITROFOL® AI as liquid carrier

Bacillus velezensis and Trichoderma harzianum are relevant microorganisms used in viticulture as biocontrol agents against pathogens of trunk (e.g. Phaeoacremonium minimum), leaves (e.g. Plasmopara viticola) or fruit (e.g. Botrytis cinerea), or as biostimulants, improving the resilience of plants against biotic or abiotic stressors through different direct and non-direct interactions.
In this biotechnological approach, formulation plays a crucial role. Controlling water activity in the product, thus stabilising microbial viability is key to ensuring effective application. We present the benefits of the citrate ester CITROFOL® AI (triethyl citrate) as a novel bio-based carrier liquid in microbial formulations. CITROFOL® AI is safe for humans and the environment, thus offering a promising base for sustainable treatments in viticulture.

Phenolic extraction during fermentation as affected by ripeness level of Syrah/R99 grapes

L’extraction phénolique au cours de la fermentation à partir de vendanges de différents degrees de maturité du cépage Syrah/R99 a été etudiée. Cette travail fait parti d’un projet focalisé sur la qualité du raisin et des vins obtenus au cours du millésime 2002. Les vignes sont situées à Stellenbosch (Afrique du Sud) sur un sol Glenrose

Innovative approaches in the evaluation of the spatial and temporal biodiversity of grape varieties from the Portuguese Bairrada appellation using LIMM-PCA: a study across five harvests

Sustainable viticulture and winemaking continue to represent huge challenges, where a better knowledge about the functional role of biodiversity in the vineyard and wine ecosystems is required, as well as the varieties plasticity. Particular attention should be devoted to the spatial and temporal interactions between authorized or recommended varieties for a specific demarcated region and clime and vineyard conditions (such as soil type, orientation of the lines, age of the vine, density of planting, harvesting practices, among others).

Dry leaf hyperspectral reflectance predicts leaf elemental composition in grafted hybrids

Elemental composition, measured as the concentrations of different elements present in a given tissue at a given time point, is a key indicator of vine health and development. While elemental composition and other high-throughput phenotyping approaches yield tremendous insight into the growth, physiology, and health of vines, costs and labor associated with repeated measures over time can be cost-prohibitive. Recent advances in handheld sensors that measure hyperspectral reflectance patterns of leaf tissue may serve as an affordable proxy for other types of phenotypic data, including elemental composition. Here, we ask if reflectance patterns of dried Chambourcin leaf tissue from an experimental grafting vineyard can predict the known elemental composition of those leaves.