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…

Macromolecular characterization of disease resistant red wine varieties (PIWI)

Pilzwiderstandsfähige (PIWI) are disease resistant Vitis vinifera interspecific hybrid varieties that are receiving increasing attention for ability to ripen in cool climates and their resistance to grapevine fungal diseases. Wines produced from these varieties have not been characterized, especially regarding their macromolecular composition. This study characterised and quantified colloid-forming molecules (proteins, polysaccharides and phenolics) of red PIWI wines produced in the UK. METHODS: In 2019 6 wines were made from the PIWI varieties Rondo, Cabernet Jura, Cabernet Cortis, Cabernet Noir, Regent and Cabertin grown at the Plumpton Rock Lodge Vineyard in Sussex (UK) and harvested at similar level of maturity (TSS, pH and TA). All juice was chaptalized to the same potential alcohol of 12%. Small scale winemaking (1L) was performed in quadruplicate using Bodum® coffee plungers to manage maceration [1]. Residual sugar content, pH, and titratable acidity were monitored during fermentation. For finished wines, the protein and polysaccharide content was measured by HPLC-SEC [2], while the total phenolic content was assessed using the Folin-Ciocalteau method [3]. The protein profile of the wines was further investigated by SDS-PAGE [4]. RESULTS: Fermentations (n=24) were all carried out to completion within 8 days.

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].

HOLISTIC APPROXIMATION OF THE INFLUENCE OF SACCHAROMYCES STRAINS ON WINE AROMA PRECURSORS

Wine varietal aroma is the result of a mixture of compounds formed or liberated from specific grape-aroma precursors. Their liberation/formation from their specific precursors can occur spontaneously by acid catalyzed rearrangements or hydrolysis or by the action of the yeast enzymatic activities. The influence of yeast during fermentation on the production of these volatile compounds has been widely studied however, the effect of this influence during aging is not fully understood. In order to evaluate these processes several indirect strategies have been used to study aroma precursors although they are not useful to understand the chemistry of the process.

Terroir et marché : exemples de stratégie pour les vins d’une petite région (Muscadet – Anjou – Touraine)

The designations of origin of the Loire Valley wine have been recognized according to customs and notoriety established over the centuries since the Middle Ages. There are four main production basins going up the Loire, from Nantes to the Sancerrois region: Nantes, Anjou-Saumur, Touraine and the vineyards of the Centre. In each of these basins, there is a wide range of appellations of origin which has been established according to a logic which may not seem obvious to the uninformed.

Wines produces without SO2 addition: which impact on their colour? An approach at the global and pigments levels

Since the 18th century, sulfur dioxide (SO2) is used in winemaking. Added at different steps, its antimicrobial but also antioxidasic and antioxidant properties are very helpful for winemakers. Nevertheless sulfur dioxide has a real potential health impact, particularly for sensitive consumers often highlighted by hygienists. Nowadays, a serious trend for “natural” wines (i.e. produced without any additives), as described by their producers, could be observed on the French market what match with a proliferation of wines elaborated without any sulfite addition.