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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.)

 

Genome assemblies

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

Haploid version: 1,409 scaffolds covering  814 Mb 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

 

Genome assemblies statistics

Oak genome assemblies V1_2N (Plomion et al. 2016) V2_2N (diploid version 2) PM1N (haploid version)
Pseudomecule Unassigned scaffolds All scaffolds
Assembly size (bp) 1,354,311,717 1,455,104,916 716,731,785 97,636,684 814,282,569
# Scaffolds 17,910 8,827 12 Chr (871 scaffolds) 538 1,409
L50 (bp) 256,640 821,707 57,352,617 621,902 1,342,530
N50  1,468 537 5 37 192
L90 (bp) 35,065 198,501 44,977,106 96,968 333,129
N90  6,626 1,880 10 195 649
Max length (bp) 1,922,255 5,542,037 115,639,695 2,943,817 5,871,596
Min length (bp) 2003 2000 39,860,516 2,095 2095
#N (% assembly) 156,586,910 (11.6%) 67,010,588 (4.6%) 20,278,712 (2.8%) 3,790,126 (3.9%) 23,989,938 (2.9%)

 

Gene prediction statistics

  PM1N (haploid version)
#Genes 25808
Gene space (Mb) 75
Gene mean / median size (bp) 2,907 / 2,137
CDS mean / median size (bp) 1,174 / 942
#Polypeptide < 500 bp 4,367
#Polypeptide > 3Kb 1,162
#genes with introns 20,297 (79%)
# introns per gene 3.3

 

Its variability

  • 31.9 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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