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

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.

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.

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.