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…

Alimentary film to reduce cork taint and improve wine organoleptic quality

Wine quality may be compromised by mouldy off‒flavours related to cork taint. Although different compounds are considered to be involved in this wine defect, haloanisoles (HAs), and among them the 2,4,6-trichloroanisole (TCA), are claimed as the main responsible.

Adapting wine production to climate change through the exploration of the diversity of Vitis vinifera cultivars

Major factors involved in wine quality and typicity are soil type, climatic conditions, plant material (rootstock and cultivar), vineyard management practices and winemaking conditions.

Impact of enological enzymes on aroma profile of Prosecco wines during second fermentation and sur lie aging

Proseccco is a famous italian Protected Designation of Origin (PDO) produced in two regions: Veneto e Friuli Venezia Giulia, however, the production is mainly concentrated in the province of Treviso. These territories are characterized by plains with some hilly areas and temperate climate. Its Production regulation provides a minimum utilization of 85% of Glera grapes, a local white grape variety, and up to a maximum of 15% of other local and international varieties. Prosecco second fermentation takes place, according to the Charmat method, in autoclaves.

MOUSY OFF-FLAVOURS IN WINES: UNVEILING THE MICROORGANISMS BEHIND IT

Taints and off-flavours are one of the major concerns in the wine industry and even if the issues provoked by them are harmless, they can still have a negative impact on the quality or on the visual perception of the consumer. Nowadays, the frequency of occurrence of mousy off-flavours in wines has increased.
The reasons behind this could be the significant decrease in sulphur dioxide addition during processing, the increase in pH or even the trend for spontaneous fermentation in wine. This off-flavour is associated with Brettanomyces bruxellensis or some lactic acid bacteria metabolisms.

Methyl Jasmonate Versus Nano-Methyl Jasmonate: Effect On The Stilbene Content In Monastrell Variety

Stilbenes, a kind of non-flavonoid phenolic compounds, have been reported to be responsible for various beneficial effects. Their biological properties include antibacterial and antifungal effects, as well as cardioprotective, neuroprotective and anticancer actions (Guerrero et al. 2009).Several strategies can be used to increase stilbene content in grapes and one of them could be the use of elicitors such as methyl jasmonate. The use of this elicitor has been proven to be efficient in the production of secondary metabolites which increases the quality of wines, but its use also has some drawbacks such as its low water solubility, high volatility, and its expensive cost (Gil-Muñoz et al. 2021).