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 


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.


Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Poster


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*


Bioinformatics, genome annotation, grapevine, Grapedia, PN40024


IVES Conference Series | Open GPB | Open GPB 2024


Related articles…

Reduced berry skin epi-cuticular wax and cutin accumulation associates with a genomic deletion and increased polyphenols extractability in a clone of Tempranillo Tinto 

Tempranillo Tinto (TT) is the third-most planted red wine variety in the world, and it is mostly grown in the Iberian Peninsula. Spontaneous somatic variation appearing during vegetative propagation can be exploited to improve elite varieties as Tempranillo Tinto, including the selection of new phenotypes enhancing berry quality. We described previously that a somatic variant of TT with darker fruit color, the clone VN21, exhibits increased extractability of polyphenols during the winemaking process. To unravel the molecular mechanism underlying this phenomenon, we performed whole-genome resequencing to compare VN21 to other TT clones, revealing a 10 Mb deletion in chromosome 11 that likely affected only the L1 meristem cell layer of VN21 and tissues derived from it, such as external cell layers of berry skin.

Water deficit impacts grape development without dramatically changing thiol precursor levels

The use of new fungus disease-tolerant grapevine varieties is a long-term and promising solution to reduce chemical input in viticulture. However, little is known about the effects of water deficit (WD) on the thiol aromatic potential of new varieties coming up from breeding programs. Varietal thiols such as 3-sulfanylhexan-ol (3SH), 4-methyl-4-sulfanylpentan-2-one (4MSP) and their derivatives are powerful aromatic compounds present in wines coming from odorless precursors in grapes, and could contribute to the wine typicity of such varieties.

Feminin vs masculin: the sensorial opposition between chambolle-musigny and gevrey-chambertin wines and the socioeconomical construction of a terroir/taste wine paradigm

At least since de XIXth century, wine writers oppose quite often the wines from Gevrey-Chambertin to the wines from Chambolle-Musigny claiming that the former are more “masculine” (full-bodied, powerful tannins, leathery, rustic…) and the later more “feminine” (delicate, elegant, silky, flowery…).

Contribution of soil and atmospheric conditions to leaf water potential in grapevines

Etant lié au sol et aux conditions atmosphériques, le statut hydrique influence la physiologie de la vigne d’une part, mais joue aussi un role important en ce qui concerne la qualité du raisin et donc du vin d’autre part. Nous avons mesuré, dans la région de Stellenbosch, le statut hydrique sur des pieds de Sauvignon Blanc non irrigués, implantés sur 2 terroirs différents, l’un froid, l’autre plus chaud.

The terroir of Pinot noir wine in the Willamette valley, Oregon – a broad analysis of vineyard soils, grape juice and wine chemistry

Wine-grapes in the Willamette Valley, Oregon, are grown on three major soil parent materials: volcanic, marine sediments, and loess/volcanic.