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…

Changes in white wine composition after treatment with cationic exchange resin: impact on wine oxidation after 8 years of bottle storage

Samples from 3 wine types were treated with a cationic exchange resin (7 lots) and stored for 8 years (47 samples). Forty-seven parameters were determined, including (1) important substrates with impact in white wine oxidation and (2) markers of oxidation. From group 1, sugars, elements, phenolic compounds, α-dicarbonyls and SO2 and from group 2, browning (A420), acetaldehyde, alkanals, furanic compounds were quantified.

Contribution of grape seeds to evolution of acetaldehyde, pigments and tannins reactive towards salivary proteins of red wine over time

This study investigated the impact of the gsk/gse ratio on the evolution of acetaldehyde and of major phenolic compounds of aglianico wine in wine like solution and real wine. Four model solutions and the correspondant control wines were prepared. The natural weight ratio between grape skins and seeds was determined on the real grapes, and a control wine was obtained from those.

DISCRIMINATION OF BOTRYTIS CINEREA INFECTED GRAPES USING UNTARGE-TED METABOLOMIC ANALYSIS WITH DIRECT ELECTROSPRAY IONISATION MASS SPECTROMETRY

Infection of grapes (Vitis vinifera) by Botrytis cinerea (grey mould) is a frequent occurrence in vineyards and during prolonged wet and humid conditions can lead to significant detrimental impact on yield and overall quality. Growth of B. cinerea causes oxidisation of phenolic compounds resulting in a loss of colour and formation of a suite of off-flavours and odours in wine made from excessively infected fruit. Apart from wine grapes, developing post-harvest B. cinerea infection in high-value horticultural products during storage, shipment and marketing may cause significant loss in fresh fruits, vegetables and other crops. A rapid and sensitive assessment method to detect, screen and quantify fungal infection would greatly assist viticultural growers and winemakers in determining fruit quality.

Is it relevant to consider remote sensing information for targeted plant monitoring?

An experiment was carried out to test the relevance of using satellite images (NDVI) to define locations of plant monitoring systems.

Ecodesign tools and approaches in viticulture for professionals and learners, contributions of the Vitarbae project

The agro-ecological transition in winegrowing can benefit from the environmental assessment of practices to inform producers’ technical choices. life cycle assessment (lca) evaluates the environmental impact of a product over its entire life cycle. this paper takes a look at the tools available for the detailed assessment and eco-design of winegrowing practices, their uses and developments in the vitarbae research project (2023-2026). this project aims to establish and equip support and training courses for the agroecological transition in viticulture and fruit arboriculture.