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…

Towards a regional mapping of vine water status based on crowdsourcing observations

Monitoring vine water status is a major challenge for vineyard management because it influences both yield and harvest quality. It is also a challenge at the territorial scale for identifying periods of high water restriction or zones regularly impacted by water stress. This information is of major importance for defining collective strategies, anticipating harvest logistic or applying for irrigation authorisation. At this spatial scale, existing tools and methods for monitoring vine water status are few and often require strong assumptions (e.g. water balance model). This paper proposes to consider a collaborative collection of observations by winegrowers and wine industry stakeholders (crowdsourcing) as an interesting alternative. Indeed, it allows the collection of a large number of field observations while pooling the collection effort. However, the feasibility of such a project and its interest in monitoring vine water status at regional scale has never been tested.

The objective of this article is to explore the possibility of making a regional map of vine water status based on crowdsourcing observations. It is based on the study of the free mobile application ApeX-Vigne, which allows the collection of observations about vine shoot growth. This information is easy to collect and can be considered, under certain conditions, as a proxy for vine water status. This article presents the first results obtained from the nearly 18,000 observations collected by winegrowers and wine industry stakeholders during 2019, 2020 and 2021 seasons. It presents the vine shoot growth maps obtained at regional scale and their evolution over the three vintages studied. It also proposes an analysis of the factors that favoured the number of observations collected and those that favoured their quality. These results open up new perspectives for monitoring vine water status at a regional scale but above they provide references for other crowdsourcing projects in viticulture.

Hemisynthesis, NMR Characterization and UHPLC-Q-Orbitrap /MS² identification of (+)-Catechin oxidation products in red wines and grape seed extracts

(+)-Catechin—laccase oxidation dimeric standards were hemi-synthesized using laccase from Trametes versicolor in a water-ethanol solution at pH 3.6.

Characterization of four Chenin Blanc-rootstock combinations to assess grapevine adaptability to water constraint

Climate change impacts water availability for agriculture, notably in semi-arid regions like South Africa, necessitating research on cultivar and rootstock adaptability to water constraints. To evaluate the performance (vegetative and reproductive) of different Chenin Blanc-rootstock combinations to the two water regimes, a field experiment was established in a model vineyard at Stellenbosch University, South Africa. Chenin Blanc vines grafted onto four different rootstocks (110Richter, 99Richter, 1103Paulsen and US 8-7) were planted in 2020. The vines are managed under two contrasting water conditions – dryland and irrigated (industry norm).

Fast, and full microbiological wine analysis using triple cellular staining.

We propose here a brand new large routine microbiological analysis method intended for oenology, in flow cytometry, using high performance equipment and triple selective cell staining, activated by fluorescence. The results and practical applications of the method are presented: Brettanomyces (Dekkera) Monitoring, fermentations monitoring, bottling and enological practices monitoring.The method allow a complete new microbiological tool for wine industry.The method has been accredited ISO 17025 in our laboratories.

Removal of white wine heat unstable proteins by using proteases and flash pasteurization-comparison with bentonites treatments

White wine protein haze can be prevented by removing the grape juice proteins, currently achieved by bentonite addition. To avoid wine volume loss and to minimizes aroma stripping, degrading haze-forming proteins in wine with proteases is a particularly interesting alternative to bentonite. In the present study, two fungal proteases treatments combined with different heating (50, 60, 72 °C) + refreshing steps, were applied on Gewürztraminer grape juice, and compared to bentonite treatments. The impact of these 19 treatments on the wine haze risks was determined by using two heat tests at 50 °C (heating during 30 to 120 min) and 80 °C (heating during 5 to 60 min). The protein contents and compositions were also estimated using the SDS-PAGE + densitometric integration techniques.