Blanc SVSE 6 - Blanc - SVSE 6 - Génomique, génétique, bioinformatique et biologie systémique

Sequencing of the oak genome and identification of genes that matter for forest tree adaptation – GENOAK

Identification of genes that matter for oak tree adaptation

The research question focuses on understanding the genetic and molecular bases of tree adaptation to their environment, a particularly relevant issue as these perennial organims will have to face with abrupt climate change at the scale of few or a single tree generation!

When adaptation and speciation mixed up

Tree adaptation to climate change will depend on both their phenotypic plasticity and standing genetic variation. The objective of the project is to identify genes of adaptation by combining the holistic approaches of evolutionary ecology tothe high throughput genomic technologies. In a first step we will decipher the genetic blue print of pedunculate oak (Quercus robur, 2n = 2x = 24, 740MB / C) by establishing a reference sequence of its genome. In a second step this genome will be structurally and functionally annotated and made available to the scientific community through a genome browser. Finally, the resequencing of several genotypes of species complex of European white oak (pedunculate, sessile, Pyrenean, pubescent) adapted to very different soil and climatic conditions, will allow to identify genes subject to natural selection and involved in their ecological divergence. This model where speciation is a by-product of adaptation to different ecological niches suggests that the inter-specific hybridization helps to homogenize the genomes of sympatric species, while the target genes of adaptation to the environment are under divergent selection and thus show unbalanced allele frequencies between species. By studying 4 sister species, one should also be able to detect generic mecanisms involved in «non-ecological« reproductive isolation.

High-throughput sequencing of a single oak tree will provide enough data to assemble DNA sequences thus establishing a reference genome.
In parallel, a high density genetic linkage map will be built on the basis of four full-sib progenies genotyped using 9000 markers. It will be aligned to the reference genome to associate chromosomal regions (QTL) involved in the genetic control of adaptive traits (water use efficiency, phenology of the apical bud ...) to known function DNA sequences. Finally, the resequencing of individuals of four sympatric oak species adapted to different ecological niches, coupled with the alignment of these sequences to the reference genome and the analysis of interspecific divergence at the nucleotide level should help to identify hot spots of genomic divergence between these inter-fertile species. These islands of speciation would bear, according to our hypothesis, alleles conferring adaptation to different environmental conditions. The comparative analysis of four species should made it possible to disentagle genes involved in reproductive isolation to those actually involved in ecological divergence.

The work and results achieved during the first 30 months, have four components. A first objective was to obtain a reference sequence of the oak genome. To this end, the genome was cut into fragments of varying size which were then sequenced by pyrosequencing «454« on the one hand and sequencing by synthesis «illumina« on the other hand. The assembly of this information has been completed, providing a first release of the oak genome (16,000 scaffolds from which 4,500 contain most of the genes). In parallel, the oak transcriptome was sequenced and assembled. This annotated unigene is used to answer several research questions in functional and evolutionary genomics. It is also be very useful to validate genes predicted from the functional annotation of the genome sequence. We also completed the construction of a genetic linkage map based on 11,000 gene loci which in turn has enabled to acquire innovative results regarding the genomic location of loci involved in reproductive isolation as well as the extent of macro-synteny with other eudicot sequenced genomes. The central question of the identification of genomic regions involved in ecological speciation was treated at the centiMorgan scale and can is now addressed at the genomic level, the four target species of this project (four sister species of European white oak living in sympatry) being already resequenced.

Ultimately, this project will provide the scientific basis for the development of diagnostic tools of the adaptive potential of oak through the analysis of nucleotide diversity of genes thus identified.

• Petit RJ, Carlson J, Curtu L, Loustau ML, Plomion C, Rodriguez AG, Sork V, Ducousso A (2013). Fagaceae trees as models to integrate ecology, evolution and genomics. New Phytol 197: 369-371
• Plomion C, Fievet V (2013) Oak genomics takes off and enters the ecological genomics era. New Phytol 199: 308-310

Trees are an important component of the global ecosystem. They dominate many regions of the world as natural, extensively or intensively managed plantations.

The Fagaceae family comprises about 1,000 woody species distributed throughout the northern hemisphere. About half belong to the Quercus (oak) genus. These oaks have traditionally high cultural and societal values. As other forest tree species, they are also providing important environmental (carbon sequestration, water cycle, reservoir of biodiversity, soil protection...) and economic (carpentry, furniture, cabinet making, veneer, cask industry, fuelwood, hunting and fungus gathering) services. Finally these long-lived organisms are considered as relevant models to study both short and long term adaptation mechanisms to abiotic and biotic constraints associated with global change, as they grow under a wide range of environments (soil and climate).

Due to their biological dominance, their commercial and ecological importance worldwide, an international network was launched recently to develop a coordinated strategy to sequence several Fagaceae genomes. These genomic resources will allow to discover which genes are involved in the adaptation of these organisms to their environments and to study their adaptive potential under current and future climate changes. In Europe, genomic resources have been developed for sessile and pedunculate oaks in the frame of the EVOLTREE network of excellence. In US, American and Chinese chestnuts (Castanea) were the main targets of an NSF funded project. Their genome is now being sequenced within Forest Health Initiative. In China, the efforts to sequence the Lithocarpus and Castanopsis genomes are also on the right track.

The present project aims at supporting the participation of French Institutions involved in this international effort. It is a collaboration between six INRA research units and the GENOSCOPE: the French National Sequencing Center. To this end our objectives are three fold: i/ to obtain a reference sequence for the pedunculate oak genome. Sequencing of a genome like oak (740Mb/C) is indeed becoming possible at a substantially reduced cost due to breakthroughs in sequencing technologies and advances in bioinformatic, ii/ annotate the genome and make the data and results available to the scientific community through interoperable databases, and iii/ identify genes that matter for forest tree adaptation through the resequencing of several genomes of sympatric species (sessile, pedunculate, pubescent and pyrenean oaks) adapted to different edapho-climatic environments. This knowledge should contribute to develop molecular tools to assess the adaptive potential of these species through the analysis of their nucleotide diversity.

Project coordination


The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


CEA COMMISSARIAT A L'ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES - Direction des Sciences du Vivant - Institut de Génomique

Help of the ANR 664,000 euros
Beginning and duration of the scientific project: September 2011 - 48 Months

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