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…

The effect of ecological conditions on the germination of pollen, fecundation and yield of some grapevine cultivars in Skopje region, Republic of Macedonia

The ecological conditions (climatic factors and soil) during the whole year, and especially before flowering and during the time of flowering, have a great influence on the functional ability of pollen, the pollination, the fecundation and the yielding potential of the cultivars of grapevine.

NOVEL BENZENETHIOLS WITH PHENOLS CAUSE ASHY, SMOKE FLAVOR PERCEPTION IN RED WINES

Smoke impacts on wines are becoming a worldwide problem; the size and severity of wildfires increasing due to influences from changing climates.¹ For over a century, wines have been known to have a unique issue of absorbing chemical compounds derived from wildfire smoke wherein the flavor of the subsequent wine becomes ashy, rubbery, campfire-like, and smoky.² The economic impacts of a smoke-impacted wine can last for years depending on the grape varietal, costing Oregon and Washington states in the United States over a billion dollars from the 2020 wildfires, as an example.³ While years of research have indicated elevated concentrations of smoke-related compounds, such as guaiacol and syringol, in wines after smoke events, unfortunately, replicating the sensory experience using smoke-associated phenols has not had much success.⁴

New acylated flavonols identified in the grape skin of Vitis vinifera cv. Tannat and their wines

Flavonols are a class of flavonoid compounds derived from plant secondary metabolism. There they play different roles like antioxidants, internal regulators and UV screenings. In red wines, flavonols have increasingly received consideration by part of scientific and winemakers according their properties began to arise known. Among these stand out wine colour stabilization and their value as bioactive compounds. In this work the complete series of the acetylated and p-coumaroylated derivatives of the 3-O-glycosides of methoxylated flavonols, namely isorhamnetin, laricitrin and syringetin, have been identified in grapes and their respective wines from Vitis vinifera cv. Tannat.

α-Terpinyl ethyl ether: stereoselective GC × GC confirmation and identification of its precursors in wine

Wines exhibit profound chemical complexity which arise from a diverse array of compounds that contribute to its sensory profile.

The state-of-the-art of grapevine biotechnology and new breeding technologies (NBTS)

 The manipulation of the genetic basis controlling grapevine adaptation and phenotypic plasticity can be performed either by classical genetics or biotechnologies.