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…

Exploring the presence of oligopeptides in wines into identify possible compounds with umami or kokumi properties

Umami is defined as a pleasant and savory taste derived from glutamate, inosinate and guanylate, which are naturally present in meat, fish, vegetables and dairy products. The term “kokumi” refers to a complex flavour sensation, characterized by thickness, fullness and continuity.

Une procédure de mise à jour des zones AOC

In France, one of INAO missions is to delimit the production area of the « Appellations d’origine contrôlées » (AOC). For wine AOC, the delimitation of plots allows for identifying plots of land that respond to technical criteria of the vine location, criteria adapted in every appellation. Some old delimitations AOC are not in adequacy with their territory. Indeed, in spite the existence of a politic aiming to protect production areas AOC, urbanization, road infrastructure or quarries occupy surfaces classified in AOC today.

Haplotype-Resolved genome assembly of the Microvine

Developing a tractable genetic engineering and gene editing system is an essential tool for grapevine. We initiated a plant transformation and biotechnology program at Oregon State University using the grape microvine system (V. vinifera) in 2018 to interrogate gene-to-trait relationships using traditional genetic engineering and gene editing. The microvine model is also used for nanomaterial-assisted RNP, DNA, and RNA delivery. Most reference genomes and annotations for grapevine are collapsed assemblies of homologous chromosomes and do not represent the specific microvine cultivar ‘043023V004’ under study at our institution.

Impact of drought stress on concentration and composition of wine proteins in Riesling

Protein haze in white wines is a major technological and economic problem of the wine industry. Field tests were carried out in steep slope vineyards planted with Riesling grapes over 3 dry growing seasons to study the effect of drought stress on the concentration of proteins in the resulting wines. Plots suffering from drought stress were compared with surrounding drip irrigated plots. Riesling grapes were processed into wines by conventional procedures. Protein amounts of the isolated wine colloids of the stressed samples were always higher than those of the watered samples(mean watered 13.8 ± 0.44, mean stressed 17.4 ± 0.40 g 100 g-1). As a consequence, higher bentonite doses were needed to achieve protein haze stability of the drought stressed treatments.

Impact of Metschnikowia pulcherrima and Saccharomyces cerevisiae in mixed fermentation on volatile compounds and energy sustainability in Lugana wine

In recent years, heightened awareness of the environmental impact has led to sustainability as a key issue for the winemaking sector.