Exploring the Vanilla planifolia genome using bioinformatics tools such as the Vanilla Genome Hub

Droc Gaëtan, Piet Quentin, Sarah Gautier, Bocs Stéphanie. 2024. Exploring the Vanilla planifolia genome using bioinformatics tools such as the Vanilla Genome Hub. In : Book of abstracts, 5th International Vanilla Congress, 4-7 June 2024, Reunion Island, France. CIRAD, Université de la Réunion. Saint-Pierre : CIRAD-Université de la Réunion, Résumé, p. 27. International Vanilla Congress (IVC 2024). 5, Saint-Pierre, Réunion, 4 Juin 2024/7 Juin 2024.

Résumé : Among tropical crops, the tricky Vanilla planifolia genome has been sequenced. Two haplotype-level genomes were produced: Daphna cultivar in 2020 and CR0040 cv in 2022. To explore CR0040, we developed a genomic portal https://vanilla-genome-hub.cirad.fr. First, we will present the Genome Hubs, knowledge systems based on generic and modular web applications such as those of the GMOD project or the South Green bioinformatics platform. We will then examine this genome version in relation to the 16-chromosome structure, the process of partial endoreplication (PE) and the orchid ancestral whole genome duplication (alpha-o WGD). Using advanced-search and browsing tools, we will identify candidate genes relevant to the vanilla value chain. For instance, we will look for protein genes involved in the biosynthesis of shikimate derivatives (phenylpropanoid metabolism), such as methyltransferases. aldehyde lyases (e.g. 4HBS, VAN), also part of the vanillin pathway, contribute to the aromatic bouquet of vanilla. Additionally, we will search for transcription factors involved in regulating flowering and fruit development (e.g. MADS-box in pod dehiscence). Building on this experience, we are considering developing a new version of the Vanilla Genome Hub to explore genetic diversity within the Vanilla genus as part of ongoing omics projects. These tools will contribute to a shared understanding of the evolution of this genus within orchids and to vanilla improvement.

Mots-clés libres : Vanilla planifolia, Bioinformatics, Comparative genomics, Metabolic pathway, Regulatory network

Auteurs et affiliations

• Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1849-1269
• Piet Quentin, Université de la Réunion (REU)
• Sarah Gautier, INRAE (FRA)
• Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426

Source : Cirad-Agritrop (https://agritrop.cirad.fr/609782/)

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