CONTACT  |  SITE MAP  |  ABOUT US   
Ask an account

About us

You are here : Home / Home URGI / About us / Publications / 2014 / Improvement of the Grapevine genome assembly

2014

International,  COM (posters)

Plant and Animal Genome Conference 2014, San Diego, CA, USA

08 Jan 2014   Improvement of the Grapevine genome assembly
poster PAG 2014 genome assembly

A. Canaguier1, S. Scalabrin2, M-C. Le Paslier3, E. Duchêne4, N. Mohelibi5, A. Berard3, A. Chauveau3,D. Scaglione2, C. Del Fabbro2, F. Cattonaro2, S. Vezzulli9, J-M. Boursiquot6, G. Di Gaspero2, L. Hausmann7, J.M. Martinez-Zapater8, M. Morgante2, A-F. Adam-Blondon5

1 INRA, UMR1165 URGV, 2 rue Gaston Crémieux, BP 5708, 91057 Evry, France

2 IGA, via J.Linussio 51, 33100 Udine, Italy

3 INRA, US1279 EPGV, CEA-IG/CNG, 2 rue Gaston Crémieux, BP 5724, 91057 Evry, France

4 SVQV, INRA, 28 rue de Herrlisheim, BP 20507, 68021 COLMAR Cedex, France

5 INRA, UR1164 URGI, route de Saint-Cyr, RD 10, 78026 Versailles, France

6 Montpellier SupAgro, INRA UMR 1334 AGAP, 2 place Pierre Viala, 34060 Montpellier, France

7 JKI, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany

8 ICVV, CSIC, UR, Gobierno de La Rioja, Madre de Dios 51, 26006, Logroño, Spain

9 Fundazione Edmund Mach, San Michele Al Adige, Italy

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

In ProdINRA

Update: 30 Sep 2016
Creation date: 08 Jan 2014