terclim by ICS banner
IVES 9 IVES Conference Series 9 A comprehensive and accurate annotation for the grapevine T2T genome 

A comprehensive and accurate annotation for the grapevine T2T genome 

Abstract

Addressing the opportunities and challenges of genomics methods in grapevine (Vitis vinifera L.) requires the development of a comprehensive and accurate reference genome and annotation. We aimed to create a new gene annotation for the PN40024 grapevine reference genome by integrating the highly accurate and complete T2T assembly and the manually curated PN40024.v4 annotation. Here, we present a novel workflow to enhance the annotation of the T2T genome by incorporating past community input found in PN40024.v4. The pipeline’s containerization will improve the workflow’s reproducibility and flexibility, facilitating its inclusion as a shared workflow on the Grapedia portal, the grapevine genomics encyclopedia. The pipeline includes both structural and functional annotation of genes, including lncRNAs and miRNAs. Moreover, we provide conversions between different annotation versions, allowing the comparison and integration of various grapevine datasets. To ensure transparency and traceability, we have modified the structure of the gene IDs, retaining the Vitvi prefix but also referencing the genome version and annotation. This will allow us to handle any gene model issues between different annotation versions and to easily distinguish the version from the annotation in publications. The annotation workflow will soon be available on the Grapedia portal (https://grapedia.org/), where it can potentially be applied to other cultivars. This annotation version will also serve as the basis for the new grape gene reference catalogue, which will provide a comprehensive and updated resource for grapevine genomics.

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Antonio Santiago1,2, David Navarro-Payá1, Pascual Villalba-Bermell1, Gustavo G. Gomez1, Iñigo De Martín Agirre1, Amandine Velt3, Marco Moretto4, Hua Xiao 5*, Yongfeng Zhou 5*, Camille Rustenholz3*, José Tomás Matus1*

1 Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46980, Valencia, Spain
2 Universitat Politècnica de València (UPV), 46022 Valencia, Spain
3 SVQV, INRAE-University of Strasbourg, Colmar 68000, France
4 Fondazione Edmund Mach Via E. Mach 1, Research and Innovation Centre, Via E. Mach 1, 38010 San Michele all’Adige, Italy
5 Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China

Contact the author*

Keywords

Bioinformatics, genome annotation, grapevine, Grapedia, PN40024

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

The estimation of the clear-sky effective PAR resources in a mountain area

Irrigation of vineyards is a matter of controversial arguments at areas of high quality wine production. Besides, the effects of the water in the plant are closer related to the water availability than to the irrigation regime.

Can early defoliation improve fruit composition of Tempranillo grapevines in the semi-arid terroir of Utiel-Requena, Spain?

Early defoliation has been found a useful tool to reduce cluster compactness and to improve fruit composition in vigorous sites of different viticultural areas. Our objective was to test the usefulness

Late frost protection in Champagne

Probably one of the most counterintuitive impacts of climate change on vine is the increased frequency of late frost. Champagne, due to its septentrional position is historically and regularly affected by this meteorological hazard. Champagne has therefore developed a strong experience in frost protection with first experiments dating from the end of 19th century. Frost protection can be divided in two parts: passive and active. Passive protection includes all the methods that do not seek to modify the vine’s environment or resistance at the time of frost. The most iconic passive protection in Champagne is the establishment of the individual reserve. This reserve allows to stock a certain quantity of clear wine during a surplus year to compensate a meteorological hazard like frost during the following years. Other common passive methods are the control of planting area (walls, bushes, topography), the choice of grape variety, late pruning, or the impact of grass cover and tillage. Active frost protection is also divided in two parts. Most of the existing techniques tend to modify vine’s environment. Most of the time they provide warmth (candles, heaters, windmills, heating cables…), or stabilise bud’s temperature above a lethal threshold (water sprinkling). The other way to actively fight is to enhance the resistance of buds to frost (elicitors). The Comité Champagne evaluates frost protection methods following three main axes: the efficiency, the profitability, and the environmental impact through a lifecycle assessment. This study will present the results on both passive and active protection following these three axes.

Optimization Of Glutathione Extraction From White Wine Lees By Doelhert Matrix

Glutathione (L-g-glutamyl-L-cysteinyl-glycine) is a tripeptide which contains three constitutive amino acids: glutamate, cysteine and glycine. It is present in plants and foods, and fruits like grapes.

Validation of the viticulture zoning methodology applied to determine the homogenous soil units present on D.O. Ribera de Duero region

The methodology to viticulture zoning developed and proposed by Gómez-Miguel and Sotés (1992) has been studied in order to validate it. This was the main aim of this work