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Tree Genetics & Genomes

, Volume 7, Issue 6, pp 1277–1285 | Cite as

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

  • Isabelle Lesur
  • Jérome Durand
  • Federico Sebastiani
  • Niclas Gyllenstrand
  • Catherine Bodénès
  • Martin Lascoux
  • Antoine Kremer
  • Giovanni G. Vendramin
  • Christophe PlomionEmail author
Original Paper

Abstract

Genomic 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.

Keywords

Quercus robur Genome composition Hypomethylated libraries SSR 

Notes

Acknowledgments

This project was supported by INRA and the European Union: a postdoctoral fellowship awarded to I. Lesur (FORESTTRAC project, no. FP7-244096) and a PhD fellowship awarded to J. Durand (EVOLTREE project, no. 16322).

Supplementary material

11295_2011_412_MOESM1_ESM.txt (82 kb)
S1 S1_SSR_hypo_random.txt—Hypomethylated and random genomic sequences containing at least one SSR (text file) (TXT 82 kb)
11295_2011_412_MOESM2_ESM.txt (93 kb)
S2 S2_nuclear_SWI_hit_hypo_random.txt—Hypomethylated and random genomic sequences potentially coding for a nuclear gene (text file) (TXT 93 kb)

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Isabelle Lesur
    • 1
  • Jérome Durand
    • 1
  • Federico Sebastiani
    • 2
  • Niclas Gyllenstrand
    • 3
  • Catherine Bodénès
    • 1
  • Martin Lascoux
    • 4
  • Antoine Kremer
    • 1
  • Giovanni G. Vendramin
    • 2
  • Christophe Plomion
    • 1
    Email author
  1. 1.INRA, UMR1202 BIOGECOCestasFrance
  2. 2.Plant Genetics InstituteNational Research CouncilFlorenceItaly
  3. 3.Department of Plant Biology and Forest GeneticsSwedish University of Agricultural SciencesUppsalaSweden
  4. 4.Evolutionary Biology CenterUppsala UniversityUppsalaSweden

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