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…

Projected impacts of climate change on viticulture over France wine-regions using downscalled CMIP6 multi-model data

Winegrape is a crop for which the quality and the identity of the final product depends strongly on the
climatic conditions of the year. By impacting production systems and the way in which wines are
developed, climate change represents a major challenge for the wine industry (Ollat et al., 2021).

Chemical and biochemical formation of polysulfides in synthetic and real wines using UHPLC-HRMS

ulfur compounds in wine have been studied for several years due to their impact on wine flavour, but the role of polysulfides is a recent topic. Polysulfides in wine are formed when two sulfhydryl groups oxidize, especially in presence of elemental sulfur or metal catalysts from field treatment residues (Ugliano et al. 2011). These compounds are odourless, but can degrade during storage and affect the wine quality. The mechanism of their formation is still largely unknown but different chemical and biochemical pathways have been suggested. Disulfides from cysteine (Cys) and glutathione (GSH) have been revealed in model wines (Kreitman et al. 2016) and more recently also higher polymerized forms in real wines (Van Leeuwen et al. 2020). Volatile varietal thiols like 3-mercaptohexanol (3MH) and 4-mercaptopentanone (4MMP) – flavour compounds with tropical or fruity notes – could undergo similar reactions, also with Cys and GSH, subsequently losing their flavour property (fate). Even more concerning is the possible release of H2S from polysulfides during storage, leading to undesired off-flavours (Sarrazin et al. 2010).

Microclimatic differences in fruit zone of vineyards on different elevations of ‘nagy-eged hill’ in eger wine region, Hungary

The Bull’s Blood of Eger (‘Egri Bikavér’) is one of the most reputed red wines in Hungary and abroad, produced in the Northeastern part of the country.

PHENOTYPIC DIVERSITY AND BIO-PROTECTION CAPABILITY OF METSCHNIKOWIA SP. IN OENOLOGY

Nowadays, the trend is to reduce the use of chemical inputs in the food sector, including in oenology. One of the inputs widely used in the wine making process are sulfites, for its several properties: antimicrobial and antioxidiant. This use isn’t without consequences on consumer’s health and environment, it can lead for example to allergic reactions and pollution. To limit the addition of chemical inputs, microbial alternatives are used. It consists to inoculate in grape must, a micro-organism able to inhibit the growth of the negative indigenous flora during the phase before the fermentation and to guarantee the sensory qualities of wines.

Manipulating grapevine bud fruitfulness

Bud fruitfulness is a key component of reproductive performance of grapevine. It plays a significant role in annual yield variation of vineyards as it is a prerequisite of crop production in the following season. Various exogenous and endogenous factors influencing the development of inflorescence primordia (IP) have been studied. However, the research on molecular genetic control of bud fruitfulness, especially how it interacts with environmental factors is still lacking. This study aims to investigate the molecular mechanism of effects of temperature and light on grapevine bud fruitfulness during initiation and differentiation of IP.