Improvement of the Grapevine Genome Assembly

The current chromosome assembly of the grapevine reference genome is under improvement using two strategies. First several maps have been densified using SNP markers developed both from a classic Sanger re-sequencing of the parents and from the re-sequencing of a panel of diversity in the Vitaceae genome to develop a 18K genotyping chip (http://urgi.versailles.inra.fr/Species/Vitis/GrapeReSeq_Illumina_20K). This allowed to develop 6 parental genetic maps that were aligned on the scaffold of the genome assembly (www.ncbi.nlm.nih.gov/assembly/317318/; urgi.versailles.inra.fr/Species/Vitis/Data-Sequences ). Second, mate paire sequences were generated from 3kb DNA fragments of V. vinifera cv. Kishmish vatkana and used for further scaffolding. We were able to improve from 85% to 89% the percentage of the ordered sequence along the chromosomes and to improve the overall orientation of the scaffolds along the chromosomes.

Acknowledgements: Grant Plant-KBBE-2008-GrapeReSeq