ArticlePlant communications2022
A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly.
Article in Plant communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- Tracing Species Boundaries Through Genomic Baits: Diagnostic SNP Panels for Genotyping Orchid Pollinaria.Evolutionary applications · 2026Article
- Orchid genome evolution and trait innovation.Journal of integrative plant biology · 2026Review
- Adaptive genomic signatures in PEBP genes reveal flowering plasticity and ecological specialization in Orchidaceae.Plant communications · 2026Article
- Nuclear genome profiling of two species ofNAR genomics and bioinformatics · 2026Article
- Genetic and Morphological Analyses of Native Vanilla Populations in Mexico Call into Question the Taxonomy ofPlants (Basel, Switzerland) · 2026Article
- A chromosome-level genome assembly of Vanilla planifolia uncovers the genomic architecture underlying partial endoreplication.BMC genomics · 2026Article
- Unraveling the Genome of Epidendrum Fulgens: Demographic History and Gene Family Dynamics in a Resilient Neotropical Orchid.Genome biology and evolution · 2026Article
- Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications.Nature communications · 2026Article
- Genome-wide identification and expression profiling of theFrontiers in plant science · 2026Article
- Comparative genetic diversity of the endangered, narrowly endemic Chinese orchidFrontiers in plant science · 2026Article
- Chromosomal-level genome assembly of the autotetraploid Anoectochilus roxburghii (Jinxianlian, Orchidaceae).Scientific data · 2025Article
- Unravelling Vanillin Biosynthesis: Integrative Transcriptomic and Metabolomic Insights intoJournal of agricultural and food chemistry · 2025Article
- Integrating genome-wide traits and multi-loci phylogeny to investigate orchid evolution-A case study on Pleurothallidinae.The Plant journal : for cell and molecular biology · 2025Article
- A chromosome-levelActa pharmaceutica Sinica. B · 2025Article
- Genome-wide characterization of PAL, C4H, and 4CL genes regulating the phenylpropanoid pathway in Vanilla planifolia.Scientific reports · 2025Article
- Comparative transcriptome profiling of vanilla (Vanilla planifolia) capsule development provides insights of vanillin biosynthesis.BMC plant biology · 2025Article
- Review
- First Gynogenesis ofPlants (Basel, Switzerland) · 2024Article
- TCOD: an integrated resource for tropical crops.Nucleic acids research · 2024Article
- Endoreplication-Why Are We Not Using Its Full Application Potential?International journal of molecular sciences · 2023Review
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18 authors.
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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.
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