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Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies
Author(s) -
Plomion Christophe,
Aury JeanMarc,
Amselem Joëlle,
Alaeitabar Tina,
Barbe Valérie,
Belser Caroline,
Bergès Hélène,
Bodénès Catherine,
Boudet Nathalie,
Boury Christophe,
Canaguier Aurélie,
Couloux Arnaud,
Da Silva Corinne,
Duplessis Sébastien,
Ehrenmann François,
EstradaMairey Barbara,
Fouteau Stéphanie,
Francillonne Nicolas,
Gaspin Christine,
Guichard Cécile,
Klopp Christophe,
Labadie Karine,
Lalanne Céline,
Le Clainche Isabelle,
Leplé JeanCharles,
Le Provost Grégoire,
Leroy Thibault,
Lesur Isabelle,
Martin Francis,
Mercier Jonathan,
Michotey Célia,
Murat Florent,
Salin Franck,
Steinbach Delphine,
FaivreRampant Patricia,
Wincker Patrick,
Salse Jérôme,
Quesneville Hadi,
Kremer Antoine
Publication year - 2016
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12425
Subject(s) - fosmid , biology , contig , genome , sequence assembly , whole genome sequencing , genome project , genetics , computational biology , reference genome , shotgun sequencing , dna sequencing , quercus robur , gene , transcriptome , botany , gene expression
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 per cent of the assembly was accounted for by 1468 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.