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OAK genome in numbers

Main characteristics

  • 12 pairs of chromosomes
  • physical size of the Quercus robur genome: 1.5Gb/2C

Kremer A, Casasoli M, Barreneche T, Bodénès C, Sisco P, Kubisiak T, Scalfi M, Leonardi S, Bakker EG, Buiteveld J, Romero-Severson  J, Arumuganathan K, Derory J, Scotti-Saintagne C, Roussel G, Bertocchi ME, Lexer C, Porth I, Hebard F, Clark C, Carlson J, Plomion C, Koelewijn HP, Villani F (2007) Fagaceae In: Genome Mapping and Molecular Breeding in Plants, Vol 7 Forest Trees, pp165-187,Chitta R Kole (Ed) Springer, Heidelberg, Berlin, New York, Tokyo (PDF : Kremer-BookKole-2007)

  • genetic size: 933 cM in 12 linkage groups with 5,460 SNPs, established using LPMerge software (PDF : Bioinformatics-2014-Endelman-1623-4), from 5.5k SNP-based genetic linkage maps (Bodénès et al. 2016, DNA Res 23:115-24.)

 

The draft genome

First version: see Plomion et al. 2016, Mol Ecol Res. 16: 254-265

Second version: available soon

Diploid version: 8,827 scaffolds covering 1.45 Gb (N50: 0.8M, L90: 1,880 scaffolds)

Haploid version: 1,409 scaffolds covering  814 Mb (N50: 1.35 Mb, L90: 649 scaffolds) and containing 25,808 high-quality protein-coding gene models (1% manually curated) and 52% of diverse Transposable Elements

Pseudomolecule: 871 scaffolds assigned to the 12 linkage groups of the genetic map, covering 716.6 Mb and containing 23,220 genes

Genome structure:

– 5 fissions and 14 fusions of the 21 eudicot ancestral karyotype to reach the modern 12-chromosome configuration

– No lineage-specific whole genome duplication

– 35.6% tandemly duplicated genes

 

Its variability

  • 33 Millions SNPs detected using whole-genome sequence data from pools of individuals of 4 species (Q. robur, Q. petraea, Q. pyrenaica, Q. pubescens) resequenced at 400X coverage.

  • 30 Millions SNPs detected using whole-genome sequence data from 18 Q. petraea populations resequenced at >100X coverage.

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