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…

Cover crops influence on soil N availability and grapevine N status, and its relationship with biogenic

The type of soil management, tillage versus cover crops, can modify the soil microbial activity, which causes the mineralization of organic N to NO3–N and, therefore, may change the soil NO3–N availability in vineyard. The soil NO3–N availability could influence the grapevine nutritional status and the grape amino acid composition. Amino acids are precursors of biogenic amines, compounds mainly formed during the malolactic fermentation. Biogenic amines have negative effects on consumer health and on the wine organoleptic quality. The objective was to study if the effect of conventional tillage and two different cover crops (leguminous versus gramineous) on grapevine N status, could relate to the wine biogenic amines composition.

Metabolomics screening of Vitis sp. interspecific hybrids to select natural ingredients with cosmetic purposes

Introducing natural ingredients using green chemistry practices is a major challenge in cosmetics industry to follow the market trend. Among the plants of cosmetic interest, vine products show a remarkable diversity of natural substances with high potential for the cosmetic and dermatological sectors. To date, research focuses on well-known compounds like E-resveratrol and E-ε-viniferin,

is the overall ecological awarness among Spanish winemakers related to their attitudes towards natural wines?

The Agenda 2030 of the EU sets out the main guidelines for transitioning towards a resilient, green and safe economy. To this regard, the wine sector is experiencing an ecological transition in different ways such as increasing the production of ecological crops, or promoting the production of wines under more environmental-friendly and healthier (i.e., lower levels of SO2) products. These alternatives to conventional production are a smaller proportion of wines, in constant growth and demand, and follow alternative and minority practices, which range from sustainable to deeply philosophical thoughts. Among these methods there are organic, biodynamic and, more recently, natural wines.

Insight on Lugana flavor with a new LC-MS method for the detection of polyfunctional thiols

The analysis of polyfunctional thiols in wine is challenging due to their low abundance and instability within a complex matrix. However, volatile thiols are highly aroma-active, making their accurate quantification in wine at low concentrations crucial [1].

Application of GiESCO “bio-metaethics” charter in practice: the “direct” involvement of vine grower, winemaker, society

On the basis of a direct agreement between the GiESCO and the vine grower, the winemaker and the consumers (individual; company; public or private organizations), the communication on the content of the charter can be done as follows:
• Commitment to respect the basic rules of the GiESCO “BIO – MetaEthics” charter.
1/ Put Mankind in the depth of all concerns in a universal context: (grower, consumer, citizen, work valuing, education, security)
2/ Insure minimum impact on environment by optimizing cultivation technics: (maximum of natural biodegradable products, friendly practices, short channels, renewable energies, terroir sustainability)