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A sample view of the pedunculate oak (Quercus robur) genome from the sequencing of hypomethylated and random genomic libraries

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLESUR, Isabelle
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDURAND, Jérôme
hal.structure.identifierNational Research Council of Italy | Consiglio Nazionale delle Ricerche [CNR]
dc.contributor.authorSEBASTIANI, Federico
hal.structure.identifierDepartment of Plant Biology and Forest Genetics
dc.contributor.authorGYLLENSTRAND, Niclas
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBODÉNÈS, Catherine
hal.structure.identifierEvolutionary Biology Center [Uppsala]
dc.contributor.authorLASCOUX, Martin
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierNational Research Council of Italy | Consiglio Nazionale delle Ricerche [CNR]
dc.contributor.authorVENDRAMIN, Giovanni G.
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
dc.date.issued2011
dc.identifier.issn1614-2942
dc.description.abstractEnGenomic resources have recently been developed for a number of species of Fagaceae, with the purpose of identifying the genetic factors underlying the adaptation of these long-lived, biologically predominant, commercially and ecologically important species to their environment. The sequencing of genomes of the size of the oak genome (740 Mb/C) is now becoming both possible and affordable due to breakthroughs in sequencing technology. However, an understanding of the composition and structure of the oak genome is required before launching a sequencing initiative. We constructed random (Rd) and hypomethylated (Hp) genomic libraries for pedunculate oak (Quercus robur) and carried out a sample sequencing of 2.33 and 2.36 Mb of shotgun DNA from the Rd and Hp libraries, respectively, to provide a first insight into the repetitive element and gene content of the oak genome. We found striking similarities between Rd sequences and previously analyzed BAC end sequences of pedunculate oak, with a similar percentage of known repeat elements (5.56%), an almost identical simple sequence repeat density (i.e., 29 SSRs per 100 kb), an identical profile of SSR motifs (in descending order of frequency—dinucleotide, pentanucleotide, trinucleotide, tetranucleotide, and hexanucleotide motifs). Conversely, the Hp fraction was, as expected, enriched in nuclear genes (2.44-fold enrichment). This enrichment was associated with a lower frequency of retrotransposons than for Rd sequences. We also identified twice as many SSR motifs in the Rd library as in the Hp library. This work provides useful information before opening a new chapter in oak genome sequencing.
dc.language.isoen
dc.publisherSpringer Verlag
dc.subjectQuercus robur
dc.subjectgenome composition
dc.subjectbibliothèque de données
dc.subjectextraction d'ADN
dc.subjectagriculture
dc.subject.enhypomethylated libraries
dc.subject.enssr
dc.subject.engenetics and heredity
dc.subject.enforestry
dc.title.enA sample view of the pedunculate oak (Quercus robur) genome from the sequencing of hypomethylated and random genomic libraries
dc.typeArticle de revue
dc.identifier.doi10.1007/s11295-011-0412-4
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalTree Genetics and Genomes
bordeaux.page1277-1285
bordeaux.volume7
bordeaux.issue6
bordeaux.peerReviewedoui
hal.identifierhal-02644223
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02644223v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Tree%20Genetics%20and%20Genomes&rft.date=2011&rft.volume=7&rft.issue=6&rft.spage=1277-1285&rft.epage=1277-1285&rft.eissn=1614-2942&rft.issn=1614-2942&rft.au=LESUR,%20Isabelle&DURAND,%20J%C3%A9r%C3%B4me&SEBASTIANI,%20Federico&GYLLENSTRAND,%20Niclas&BOD%C3%89N%C3%88S,%20Catherine&rft.genre=article


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