The 9th and 10th of November to 10, in Saint Pierre de la Réunion, the consortium of the Vanilla planifolia genome sequencing project (VANISEQ) had its closing meeting with all the partners involved.
Two companies, Eurovanille and Mane, and four public laboratories from Cirad ( UMR AGAP- SouthGreen bioinformatics platform in Montpellier and UMR PVBMT in La Reunion) and INRAE ( GeT-PlaGe and CNRGV), collaborated within the VANISEQ consortium.
The main objective of the consortium was to produce a high quality reference sequence of the Vanilla planifolia genome (2Gb, 2n=32, heterozygous). This genotype represents 90% of the world production. It is maintained in the CRB Vatel collection from Cirad.
William Marande, in charge of the VANISEQ project at CNRGV, presented our contribution to the improvement of the genome assembly.
The sequences were produced by the Get-Plage platform and assembled by SouthGreen bioinformatics platform in Montpellier.
The optical map of the genome was produced and analysed by the CNRGV.
We integrated the sequence assembly and the optical map of the genome to obtain a final continuous assembly of high quality. This work also allowed us to separate the haplotypes of this heterozygous genome.
Data assembly was complicated due to the phenomenon of partial endoreplication of the genome, an orchid-specific phenomenon that results in variations in the amount of DNA present in the cells. The long PacBio Hifi sequence reads were used to overcome this problem.
The assembled genome has been then annotated by Cirad bioinformaticians in Montpellier and La Réunion.
The data produced can be analyzed and valorized using the " genome hub" bioanalysis platform created by SouthGreen bioinformatics platform in Montpellier. This online platform provides easy access to various genome analysis tools (synteny, cell metabolic pathways, etc.). This powerful and complete tool will be made available to the community working on Vanilla.
This meeting was an opportunity to review all the results, the upcoming publication and the follow-up of the project. The production of a version 2 of the genome was proposed and the opportunity to sequence other genotypes was discussed.
For more details about the VANISEQ project: