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: Plomion et al. (2018) Nature Plants
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. Navigate on the pseudomolecule using the Oak Genome Browser : https://urgi.versailles.inra.fr/WebApollo_oak_PM1N/PseudoMolecule.html
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.
- Raw sequencing data are available here :
- 4 European white oak species (https://www.biorxiv.org/content/10.1101/246637v2) : PRJEB23847 (https://www.ebi.ac.uk/ena/data/view/PRJEB23847)
- 18 sessile oak populations (https://www.biorxiv.org/content/10.1101/584847v1): PRJEB32209 (https://www.ebi.ac.uk/ena/data/search?query=PRJEB32209) /
- SRA run IDs & population ID used in Leroy et al. 2019 SRA_EBI_accessions_sumup_correspondance