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Plant communications
09 12, 2022;3 (5): 100330.

A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly.

Quentin Piet, Gaetan Droc, William Marande, Gautier Sarah, Stéphanie Bocs, Christophe Klopp, Mickael Bourge, Sonja Siljak-Yakovlev, Olivier Bouchez, Céline Lopez-Roques, Sandra Lepers-Andrzejewski, Laurent Bourgois, Joseph Zucca, Michel Dron, Pascale Besse, Michel Grisoni, Cyril Jourda, Carine Charron
Author Information
  1. Quentin Piet: CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France.
  2. Gaetan Droc: CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France. Electronic address: gaetan.droc@cirad.fr.
  3. William Marande: INRAE, CNRGV, Genotoul, 31326 Castanet-Tolosan, France.
  4. Gautier Sarah: French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France; AGAP, Univ. Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France.
  5. Stéphanie Bocs: CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France.
  6. Christophe Klopp: Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France.
  7. Mickael Bourge: Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
  8. Sonja Siljak-Yakovlev: Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution (ESE), 91190 Gif-sur-Yvette, France.
  9. Olivier Bouchez: INRAE, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France.
  10. Céline Lopez-Roques: INRAE, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France.
  11. Sandra Lepers-Andrzejewski: Etablissement Vanille de Tahiti, Uturoa, French Polynesia, France.
  12. Laurent Bourgois: Eurovanille, Rue de Maresquel, 62870 Gouy Saint André, France.
  13. Joseph Zucca: Département Biotechnologie, V. Mane Fils, 06620 Le Bar Sur Loup, France.
  14. Michel Dron: Université Paris-Saclay, CNRS, INRAE, Univ. Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France.
  15. Pascale Besse: Université de la Réunion, UMR PVBMT, Saint-Pierre, La Réunion, France.
  16. Michel Grisoni: CIRAD, UMR PVBMT, 501 Tamatave, Madagascar. Electronic address: michel.grisoni@cirad.fr.
  17. Cyril Jourda: CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France. Electronic address: cyril.jourda@cirad.fr.
  18. Carine Charron: CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France.
PMID: 35617961 DOI: 10.1016/j.xplc.2022.100330

Abstract

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.

Keywords

genome hub optical mapping partial endoreplication vanilla whole-genome sequencing

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MeSH Term

Chromosomes
Endoreduplication
Genome Size
Haplotypes
Vanilla
Journal Article Research Support, Non-U.S. Gov't

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