Genomics and Forest Tree Genetics Conference (2016-05-30-2016-06-03) Arcachon (FRA). In : Book of abstracts. 2016. 134 p.27 Jul 2016 Oak genome sequencing and evolution
Salse, J. ; Aury, J. M. ; Murat, F. ; Faye, S. ; Labadie, K. ; Dossat, C. ; d’Agata, L. ; Da Silva, C. ; Barbe, V. ; Wincker, P. ; Klopp, C. ; Faivre-Rampant, P. ; Berges, H. ; Amselem, J. ; Quesneville, H. ; Francillonne, N. ; Bodénès, C. ; Le Provost, G. ; Lalanne, C. ; Salin, F. ; Ehrenmann, F. ; Leroy, T. ; Lesur, I. ; Kremer, A. ; Plomion, C.
Oaks are among the most impressive trees. Their long-lived nature, symbol of strength and endurance; their biological dominance, characterized by a species-rich assemblage of organisms below and above ground, make them keystone species of major ecosystem functioning. These species are ecologically and genetically very diverse, growing in extremely variable conditions throughout the northern hemisphere where they provide a wide range of environmental and economic services.To obtain a WGS assembly of Quercus robur (~ 750 Mb/C), we used a combination of i/ short reads (Illumina) from size-selected sequencing paired-end and mate-pair libraries, ii/ reads of medium length (454-Roche), iii/ synthetic long-reads (Illumina) and iv/ BAC ends (Sanger). Synthetic long-reads made it possible to better separate both haplotypes of the selected tree genotype, owing to the accumulation of polymorphisms in this highly heterozygote species. Sequences were assembled into 8,827 scaffolds (>2kb) representing 1.45 Gb, with an N50 scaffold length of 0.82 Gb. Merging both haplotypes further helped to improve contiguity. The haploid genome assembly (1,409 scaffolds), consisted of ~ 810 Mb with an N50 scaffold of 1.34 Mbp, 88% of which (represented by 876 scaffolds) were anchored to the 12 chromosomes using a high density SNP-based linkage map and a syntenome strategy using Prunus persica as a pivotal genome sequence.We then investigated the evolutionary history of the modern oak genome in comparing the 26,768 annotated genes covering 714.4 Mb anchored on the 12 pseudomolecules to that of available eudicot genomes. From the eudicot ancestor structured in 21 chromosomes and containing 7,072 protogenes, we found that the oak genome did not experience lineage-specific whole genome duplication, and harbors relics of the known ancestral (gamma) triplication (hexaploidization) shared by the eudicots. From this ancestor, the modern oak genome has been shaped trough intense chromosomal rearrangements involving ancestral chromosome fusions and fissions. At the gene level, 92 families have expanded specifically in oak, compared to fifteen other eudicot species, consisting in major gene functions operating as a vehicle for oak adaptation.