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…

Efficient irrigation strategies and water use reduction in the high quality production regions of Priorat and Montsant (Spain)

Priorat and Montsant Appellations of Origin are located in the south of Catalonia (North‐East Spain), under severe Mediterranean climatic conditions

Fresh odorous terpenoids in wines, multiples pathways of limonene degradation.

Mint aromas in wine, which manifest as “cool” or “fresh” character, can originate from different chemical classes, one of which is the terpenoids. A broadly diverse, naturally occurring class of chemical compounds, terpenes possess wide applications across multiple industries due to their pharmaceutical, antiseptic, medical, and aromatic properties. Monoterpenes, a subclass of terpenoids, likewise play a major role in wine sensory perception. Within the monoterpenes, those possessing “mint” odor qualities have often been studied in the context of “vegetal” or “herbal” wine faults; however, their role in positive aromatic evolution is less understood. Yet an extensive 2015 study of older premium Bordeaux red wines identified mint as a contributing factor in quality bouquet development. From that point, it was necessary to investigate the origins of those monoterpenes as well as the chemical conditions required for their development during ageing. Those two key points could finally facilitate predicting the apparition of minty character in older wines based on their composition while young.
A principal contributor is the cyclic monoterpene limonene, which was isolated relatively early in grapes and wine. Not only does limonene itself possess a cool, fresh odor, it is also a precursor for, and possible derivative of, additional mint monoterpenes. Among the most commonly found monoterpenes, limonene and its derivatives can constitute the majority of the essential oils of citrus fruits, mint and herb plants, and coniferous trees. Many of these mint monoterpenes also occur in grapes and wine. With aromas ranging from woody and earthy to citrus to mint and herbaceous, their contribution to wine is potentially diverse and multi-faceted. While sometimes, found at concentrations below the sensory threshold, synergistic effects between these molecules could render them perceivable.
This review looks at limonene and its transformation as studied in different matrices, and potential parallels or analogues in wine. Moreover, within the complex kinetics of wine aging, the relative concentrations of mint monoterpenes appears to continue to evolve and change, with additional evidence from model wine solutions suggesting they may even revert to their originating precursors. Continued study of mint monoterpenes and their role in wine aromatics will contribute to a deeper understanding of the development of aging bouquet and the longevity of premium wines.

A multidisciplinary approach to grapevine zoning G.I.S. technology based: an example of thermal data elaboration

Un grand nombre d’études ont été consacrées à l’évaluation quantitative des effets de climat sur la qualité des vignes, dans différents contextes climatiques. Généralement, la vocation viticole d’un terroire peut être étudiée par des approches mono ou multidisciplinaires.

The use of plasma activated water in barrel disinfection: impact on oak wood composition

The use of barrels is a practice that improves the quality of wines. The porous structure of wood favors the accumulation of microorganisms that can deteriorate the quality of wines so that barrel cleaning and sanitizing treatments are essential. The burning of sulphur discs has been the most common practice in winemaking because ots biocide effect. Nevertheless, its effectiveness is still insufficient and it is harmful for human health.

Using image analysis for assessing downy mildew severity in grapevine

Aim: Downy mildew is a crucial disease in viticulture. In-field evaluation of downy mildew has been classically based on visual inspection of leaves and fruit. Nevertheless, non-invasive sensing technologies could be used for disease detection in grapevine. The aim of this study was to assess downy mildew severity in grapevine leaves using machine vision.