A chromosome-level, haplotype-phased genome assembly for Vanilla planifolia highlights that partial endoreplication challenges accurate whole genome assembly

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, Bourgois Laurent, Zucca Joseph, Dron Michel, Besse Pascale, Grisoni Michel, Jourda Cyril, Charron Carine. 2022. A chromosome-level, haplotype-phased genome assembly for Vanilla planifolia highlights that partial endoreplication challenges accurate whole genome assembly. Plant Communications, 3:100330, 15 p.

Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/PRJNA753216 / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA754028 / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/biosample/SAMN20691751/ / Url - jeu de données - Entrepôt autre : https://vanilla-genome-hub.cirad.fr/

Résumé : Vanilla planifolia, the species cultivated to produce one of the world's most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.

Mots-clés Agrovoc : Vanilla planifolia, génome, banque de données, application des ordinateurs, cartographie chromosomique

Mots-clés géographiques Agrovoc : La Réunion, France

Mots-clés complémentaires : Séquencage, endoréduplication, genome scans (en)

Mots-clés libres : Vanilla, Whole-genome sequencing, Optical mapping, Partial endoreplication, Genome hub

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Agences de financement européennes : European Regional Development Fund

Agences de financement hors UE : Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Université de La Réunion, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Etablissement Vanille de Tahiti, Agence Nationale de la Recherche, Conseil Régional de La Réunion

Auteurs et affiliations

• Piet Quentin, CIRAD-BIOS-UMR PVBMT (REU)
• Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1849-1269 - auteur correspondant
• Marande William, CNRGV (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)
• Bourgois Laurent, Eurovanille (FRA)
• Zucca Joseph, 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 - auteur correspondant
• Jourda Cyril, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0002-7799-3501 - auteur correspondant
• Charron Carine, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0003-0281-9936

Source : Cirad-Agritrop (https://agritrop.cirad.fr/601012/)

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