A chromosome-level genome assembly of Vanilla planifolia uncovers the genomic architecture underlying partial endoreplication

BACKGROUND: Partial endoreplication is a prominent developmental feature and poses a significant challenge for whole genome assembly in orchids. This form of cell cycle results in highly unbalanced cell DNA content, with the highly endoreplicated (P) fraction being overrepresented in sequencing data compared to the non-endoreplicated (F) fraction. RESULTS: Here, we report the first genome assembly of Vanilla planifolia into 16 chromosome pairs using axillary buds enriched in non-endoreplicated 2 C-nuclei (55%) as determined by flow cytometry. The assembly was generated using a hybrid approach combining PacBio HiFi sequencing and Omni-C scaffolding generated in this study, together with a GBS-SNP genetic map and Oxford Nanopore Technologies long-read data from the literature. For the first time, we identified P and F regions within reconstructed chromosomes, representing 20.57% and 79.43% of the genome, respectively based on DNA sequencing data from three tissues with varying levels of endoreplicated nuclei. P regions were gene-rich and located at chromosome ends, whereas F regions were SSR-rich and located at central parts of chromosomes. Remarkably, 97.24% of SSRs were found in F regions, predominantly comprising the trinucleotide AAG/CTT motif, which may contribute to the absence of endoreplication in these regions. Protein-encoding genes overrepresented in F regions were associated with negative regulation of flower development, mitotic cycle progression, cell division and histone modification. CONCLUSIONS: This accurate high-quality chromosome-scale V. planifolia genome assembly provides unprecedented insights into the structural and molecular characteristics of partial endoreplication in Orchids and represents a major step toward the characterization of this complex genome.

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Journal
BMC Genomics
Published
2026-05-13
DOI
https://doi.org/10.1186/s12864-026-12926-1
Primary Topic
Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
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article
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article

A chromosome-level genome assembly of Vanilla planifolia uncovers the genomic architecture underlying partial endoreplication

Marilyne Summo, Quentin Piet, Mickaël Bourge, Michel Grisoni et al.
BMC Genomics
Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
article

A chromosome-level genome assembly of Vanilla planifolia uncovers the genomic architecture underlying partial endoreplication

Marilyne Summo, Quentin Piet, Mickaël Bourge, Michel Grisoni, Gaëtan Droc, Pascale Besse, Cyril Jourda, Fanny Lambert, Carine Charron, Charlotte Cravero, Michel Dron, Hadrien Máté de Gérando, Amaury Dedours, Olivier Bouchez, Stéphanie Bocs, Sonja Siljak-Yakovlev, Nathalie Rodde, Marine Sallaberry, Christophe Klopp, William Marande
article en

Abstract

BACKGROUND: Partial endoreplication is a prominent developmental feature and poses a significant challenge for whole genome assembly in orchids. This form of cell cycle results in highly unbalanced cell DNA content, with the highly endoreplicated (P) fraction being overrepresented in sequencing data compared to the non-endoreplicated (F) fraction. RESULTS: Here, we report the first genome assembly of Vanilla planifolia into 16 chromosome pairs using axillary buds enriched in non-endoreplicated 2 C-nuclei (55%) as determined by flow cytometry. The assembly was generated using a hybrid approach combining PacBio HiFi sequencing and Omni-C scaffolding generated in this study, together with a GBS-SNP genetic map and Oxford Nanopore Technologies long-read data from the literature. For the first time, we identified P and F regions within reconstructed chromosomes, representing 20.57% and 79.43% of the genome, respectively based on DNA sequencing data from three tissues with varying levels of endoreplicated nuclei. P regions were gene-rich and located at chromosome ends, whereas F regions were SSR-rich and located at central parts of chromosomes. Remarkably, 97.24% of SSRs were found in F regions, predominantly comprising the trinucleotide AAG/CTT motif, which may contribute to the absence of endoreplication in these regions. Protein-encoding genes overrepresented in F regions were associated with negative regulation of flower development, mitotic cycle progression, cell division and histone modification. CONCLUSIONS: This accurate high-quality chromosome-scale V. planifolia genome assembly provides unprecedented insights into the structural and molecular characteristics of partial endoreplication in Orchids and represents a major step toward the characterization of this complex genome.

BMC Genomics
Centre National de la Recherche Scientifique (FR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR), Université de Montpellier (FR), AgroParisTech (FR), University of Reunion Island (RE), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Institut des Sciences des Plantes de Paris Saclay (FR), Ecologie, Société, Evolution (FR), Institut de Biologie Intégrative de la Cellule (FR), Madagascar Biodiversity Partnership (MG), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (FR), CEA Paris-Saclay (FR), Mane (France) (FR), Peuplements végétaux et bioagresseurs en milieu tropical (RE), Institut Agro Montpelier (FR), Laboratoire de Recherche en Sciences Végétales (FR), Eurorad (France) (FR), Services déconcentrés d'appui à la recherche Occitanie-Montpellier (FR), Institute of Bioinformatics (IN), Génétique Physiologie et Systèmes d'Elevage (FR), Institut de Recherche pour le Développement (FR)
European Commission, Conseil Régional de La Réunion, European Regional Development Fund
Life in Land
Openalex Percentile: Top 7%
Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
DOIOpen Access PDFOpenAlex
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