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Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

hal.structure.identifierUnité de recherche en génomique végétale [URGV]
dc.contributor.authorFAIVRE-RAMPANT, Patricia
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLESUR, Isabelle
hal.structure.identifierUnité de recherche en génomique végétale [URGV]
dc.contributor.authorBOUSSARDON, Clément
hal.structure.identifierUnité de recherche en génomique végétale [URGV]
dc.contributor.authorBITTON, Frederique
hal.structure.identifierUnité de recherche en génomique végétale [URGV]
hal.structure.identifierMathématiques et Informatique Appliquées [MIA-Paris]
dc.contributor.authorMARTIN-MAGNIETTE, Marie-Laure
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBODENES-BREZARD, Catherine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLE PROVOST, Grégoire
hal.structure.identifierCentre National de Ressources Génomiques Végétales [CNRGV]
dc.contributor.authorBERGES, Helene
hal.structure.identifierAustrian Institute of Technology [AIT]
dc.contributor.authorFLUCH, Sylvia
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
dc.date.issued2011
dc.identifier.issn1471-2164
dc.description.abstractEnBackground : One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences. * Results : The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera. * Conclusions : This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.
dc.language.isoen
dc.publisherBioMed Central
dc.title.enAnalysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
dc.typeArticle de revue
dc.identifier.doi10.1186/1471-2164-12-292
dc.subject.halSciences du Vivant [q-bio]/Génétique
bordeaux.journalBMC Genomics
bordeaux.page13 p.
bordeaux.volume12
bordeaux.peerReviewedoui
hal.identifierhal-02646702
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02646702v1
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