Advances in reconstructing the genome of Vanilla planifolia: Addressing partial endoreplication challenges

Piet Quentin, Droc Gaëtan, Marande William, Sarah Gautier, Bocs Stéphanie, Klopp Christophe, Bourge Mickael, Siljak-Yakovlev Sonja, Bouchez Olivier, Lopez-Roques Céline, Lepers-Andrzejewski Sandra, Dedours Amaury, Lambert Fanny, Dron Michel, Besse Pascale, Grisoni Michel, Jourda Cyril, Charron Carine. 2024. Advances in reconstructing the genome of Vanilla planifolia: Addressing partial endoreplication challenges. 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. 22. International Vanilla Congress (IVC 2024). 5, Saint-Pierre, Réunion, 4 Juin 2024/7 Juin 2024.

Résumé : Despite Vanilla planifolia's economic importance, genomic resources decisive in modern diversity studies and breeding programs have been lacking. Recent attempts to reconstruct this 4.09 Gb diploid genome (16 pairs of chromosomes) revealed insights into gene (~59,000) and repeat content (72% of the genomic sequence). However, none fully succeeded in reconstructing the entire sequence, with the most complete assembly reaching 82% of the expected size and anchoring only one-third of its sequence on a total of 14 pairs of chromosomes, meaning that two pairs are still missing. In addition to frequent aneuploidy and a high rate of repeats, the main cause of the difficulties encountered seems to be partial endoreplication (PE), an orchid specific phenomenon involving several replication rounds of a fraction of the genome without cell division. PE varies in genome proportion and amplification intensity depending on the species and the tissues observed. Latest efforts from the Vaniseq consortium, leveraging tissue selection and technological advancements, are finally leading to a complete and more contiguous assembly, focusing on a better understanding of PE. All in all, this assembly and its refined annotation, along with the recent increase of Vanilla related omics data, should open up new possibilities in several fields, including vanilla varietal improvement and diversity studies.

Mots-clés libres : Vanilla planifolia, Endoreplication, Genomics, Partial endoreplication

Agences de financement hors UE : Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Projets sur financement : (REU) VANISEQ

Auteurs et affiliations

• Piet Quentin, Université de la Réunion (REU) - auteur correspondant
• Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1849-1269
• Marande William, INRAE (FRA)
• Sarah Gautier, Université de Montpellier (FRA)
• Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
• Klopp Christophe, INRAE (FRA)
• Bourge Mickael, CNRS (FRA)
• Siljak-Yakovlev Sonja, Université Paris-Saclay (FRA)
• Bouchez Olivier, INRAE (FRA)
• Lopez-Roques Céline, INRAE (FRA)
• Lepers-Andrzejewski Sandra, Etablissement vanille de Tahiti (PYF)
• Dedours Amaury, Eurovanille (FRA)
• Lambert Fanny, V. Mane Fils (FRA)
• Dron Michel, Université Paris-Saclay (FRA)
• Besse Pascale, Université de la Réunion (REU)
• Grisoni Michel, CIRAD-BIOS-UMR PVBMT (MDG) ORCID: 0000-0001-9867-9098
• Jourda Cyril, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0002-7799-3501
• Charron Carine, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0003-0281-9936

Source : Cirad-Agritrop (https://agritrop.cirad.fr/609710/)

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