Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

Mol Ecol Resour. 2015 May 6. doi: 10.1111/1755-0998.12425.

Added on : 21 May 2015

Read more

Authors :

Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A.

 

Mol Ecol Resour. 2015 May 6. doi: 10.1111/1755-0998.12425.

 

Abstract :

The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (> 2 kb) corresponding to 1.34 Gb. Fifty percent of the assembly was accounted for by 1,468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome. This article is protected by copyright. All rights reserved.

 

Links :

http://www.ncbi.nlm.nih.gov/pubmed/25944057

 

Press releases :

http://presse.inra.fr/en/Resources/Press-releases/Oak-genome-decoded

http://presse.inra.fr/Ressources/Communiques-de-presse/Le-genome-du-chene-sequence

http://www.franceinter.fr/player/reecouter?play=1094293

http://www.lesoir.be/875795/article/vins/actu-vins/2015-05-12/genome-du-chene-sequence

http://www.sciencesetavenir.fr/biologie/20150511.OBS8751/le-genome-du-chene-decrypte.html