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…

Viticultural potential assessment and its spatial delineation analysis in Goriška Brda viticultural area

Viticultural potential has a complex conditioning, determined by relief,
soil, climate and lithology. Delineation of viticultural potential from vineyard areas is essential for the purpose to collect the necessary data for viticultural zoning. Using this data, we can achieve greater yield quality, which is the most important criteria in viticulture. The main purpose of this research is
characterizing of viticultural potential and zoning of homogeneous viticultural zones in Goriška Brda region by assessing the suitability of defined ecological factors.

Technological possibilities of grape marc cell walls as wine fining agent. Effect on wine phenolic composition

Fining is a technique that is used to remove unwanted wine components that affect clarification, astringency, color, bitterness, and aroma. Fining involves the addition of adsorptive or reactive material in order to reduce or eliminate the presence of certain less desirable wine components and to ensure that a wine remains in a particular stable state for a given period of time Recently concerns have been raised about the addition of animal proteins, such as gelatin, to wine due to the disease known as bovine spongiform encephalopathy (Mad Cow disease). Although the origin of gelatins has been moved to porcine, winemakers are asking for substitute products with properties and application protocols similar to the traditional animal-derived ones, making the use of plant-derived proteins in fining a practically viable possibility. As a consequence, various fining agents derived from plants have been proposed, including proteins from cereals, legumes, and potato.

Variety and climatic effects on quality scores in the Western US winegrowing regions

Wine quality is strongly linked to climate. Quality scores are often driven by climate variation across different winegrowing regions and years, but also influenced by other aspects of terroir, including variety. While recent work has looked at the relationship between quality scores and climate across many European regions, less work has examined New World winegrowing regions. Here we used scores from three major rating systems (Wine Advocate, Wine Enthusiast and Wine Spectator) combined with daily climate and phenology data to understand what drives variation across wine quality scores in major regions of the Western US, including regions in California, Oregon and Washington. We examined effects of variety, region, and in what phenological period climate was most predictive of quality. As in other studies, we found climate, based mainly on growing degree day (GDD) models, was generally associated with quality—with higher GDD associated with higher scores—but variety and region also had strong effects. Effects of region were generally stronger than variety. Certain varieties received the highest scores in only some areas, while other varieties (e.g., Merlot) generally scored lower across regions. Across phenological stages, GDD during budbreak was often most strongly associated with quality. Our results support other studies that warmer periods generally drive high quality wines, but highlight how much region and variety drive variation in scores outside of climate.

Fungal communites diversity and functional roles of different types of Botrytis cinerea infected grape berries on different growing sites

Botrytis cinerea, an Ascomycota pathogen with a broad host range, infects over 1200 plant species. Grapes infected by this pathogen, which subsequently develop a noble rot, remain in the vineyard for an extended period, thus being exposed to a diverse array of physical, chemical and biological factors, which give rise to a complex microbial community.

Plant biostimulants in combination treatments as environmentally-friendly rest-breaking agents for dormancy release in table grapes Vitis vinifera Crimson Seedless

Context and purpose of the study. Vitis vinifera grapevine is a perennial crop which is globally cultivated, surviving cold winters in temperate zones by entering a state of dormancy.