A chromosome-level,haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate wholegenome assembly  被引量:1

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作  者:Quentin Piet Gaetan Droc William Marande Gautier Sarah Stephanie Bocs Christophe Klopp Mickael Bourge Sonja Siljak-Yakovlev Olivier Bouchez Ce line Lopez-Roques Sandra Lepers-Andrzejewski Laurent Bourgois Joseph Zucca Michel Dron Pascale Besse Michel Grisoni Cyril Jourda Carine Charron 

机构地区:[1]CIRAD,UMR PVBMT,97410 Saint-Pierre,La Reunion,France [2]CIRAD,UMR AGAP Institut,34398 Montpellier,France [3]UMR AGAP Institut,Univ Montpellier,CIRAD,INRAE,Institut Agro,34398 Montpellier,France [4]French Institute of Bioinformatics(IFB)-South Green Bioinformatics Platform,Bioversity,CIRAD,INRAE,IRD,34398 Montpellier,France [5]INRAE,CNRGV,Genotoul,31326 Castanet-Tolosan,France [6]AGAP,Univ.Montpellier,CIRAD,INRAE,Montpellier SupAgro,Montpellier,France [7]Plateforme Bioinformatique,Genotoul,BioinfoMics,UR875 Biometrie et Intelligence Artificielle,INRAE,Castanet-Tolosan,France [8]Cytometry Facility,Imagerie-Gif,Universite Paris-Saclay,CEA,CNRS,Institute for Integrative Biology of the Cell(I2BC),91198 Gif-sur-Yvette,France [9]Universite Paris-Saclay,CNRS,AgroParisTech,Ecologie Syste matique Evolution(ESE),91190 Gif-sur-Yvette,France [10]INRAE,GeT-PlaGe,Genotoul,31326 Castanet-Tolosan,France [11]Etablissement Vanille de Tahiti,Uturoa,French Polynesia,France [12]Eurovanille,Rue de Maresquel,62870 Gouy Saint Andre,France [13]De partement Biotechnologie,V.Mane Fils,06620 Le Bar Sur Loup,France [14]Universite Paris-Saclay,CNRS,INRAE,Univ.Evry,Institute of Plant Sciences Paris-Saclay(IPS2),91405 Orsay,France [15]Universite de la Re union,UMR PVBMT,Saint-Pierre,La Re union,France [16]CIRAD,UMR PVBMT,501 Tamatave,Madagascar

出  处:《Plant Communications》2022年第5期117-131,共15页植物通讯(英文)

基  金:This work was supported by France Genomique National infrastructure,funded as part of“Investissement d’avenir”program managed by Agence Nationale pour la Recherche(contrat ANR-10-INBS-09)and has also benefited from Imagerie-Gif core facility supported by l’Agence Nationale de la Recherche(ANR-11-EQPX-0029/Morphoscope,ANR-10-INBS-04/FranceBioImaging;ANR-11-IDEX-0003-02/Saclay Plant Sciences).

摘  要:Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly proneto partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report herethe 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 thediploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequentlyobserved. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gbwith a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequenciesand 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 linkinggene-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 complexmolecular regulation of endoreplication along the chromosomes. This high-quality, anchored assemblyrepresents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidationof this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a userfriendly integrated web portal that enables centralized access to high-throughput genomic and other omicsdata and interoperable use of bioinformatics tools.

关 键 词:VANILLA whole-genome sequencing optical mapping partial endoreplication genome hub 

分 类 号:Q943.2[生物学—植物学]

 

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