A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)

The grapevine reference genome was published by Jaillon et al. [1]. The sequence for the first version of the genome, called the 8X version, was obtained using a whole genome shotgun strategy and the Sanger sequencing technology and was assembled from reads representing 8X coverage. Soon after, the assembly was improved through the addition of 4X of additional coverage, including more Bacterial Artificial Chromosome end sequences that greatly improved the scaffolding of the sequence contigs [2], [3]. The corresponding scaffolds and raw sequences were deposited in European Molecular Biology Laboratory (EMBL) archives (FN594950-FN597014, 2065 entries, release 102). A new chromosome assembly was also developed, based on an improved version of the maps used for the 8X genome version [2], [3], [4], [5] and was also archived at EMBL (FN597015-FN597047, 33 entries, release 102): it is referenced in the grapevine community as the 12X.v0 version of the grapevine reference genome. The chromosome sequence scaffolding of this version still necessitated improvements as around 9% of the sequence was not anchored to chromosomes (with the corresponding scaffolds stacked in the “Unknown” chromosome) and 3.5% of the sequence could be assigned to a chromosome but without certain placement and orientation within the chromosome (stacked in additional “random” chromosomes).
This work was supported by the French National Institute for Agriculture (INRA, France), the University of Udine and the Institute of Applied Genomics (Italy), the Vlaams Institut voor Biotechnologie and the University of Ghent (Belgium), the Istituto de Ciencas de la Vid et del Vino (Logroño, Spain) and several grants: ANR-Plant-KBBE-2008- GrapeReSeq and ANR-2008-Muscares funded by the French National Research Agency (ANR), Valorizzazione dei Principali Vitigni Autoctoni Italiani e dei loro Terroir (Vigneto, no. COSVIR27129) funded by the Italian Ministry of Agriculture and the COST action FA1106 funded under the European FP7 Research Program