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Last update: May 2021

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Institut Sophia Agrobiotech

Institut Sophia Agrobiotech

UMR INRA - Univ. Nice Sophia Antipolis - Cnrs

Genomics & Adaptive Molecular Evolution

GAME logo
© etienne danchin
The GAME team studies mechanisms of genomic plasticity related to: 1 - species evolution towards a parasitic or pathogenic life style and 2 - adaptation of these same species to current environmental changes, including to methods deployed to manage them.
Scientists in GAME use bioinformatics, biostatistics and artificial intelligence for their research.

GAME: Genomics & Adaptive Molecular Evolution

Plasticity and stability of genetic information encoded in genomes is at the heart of species evolution, adaptability and ecological success. In GAME, we study mechanisms contributing to genome plasticity linked to adaptive evolution of species whose interactions have an impact on plant health.

Accompanying the democratization of DNA and RNA sequencing and technological advances in this domain, more and more massive multi-omics data (genomics, transcriptomics, epigenomics, metagenomics) become available for a diversity of species whose biology is linked to plant health.

Main questions

Genomic signatures of adaptive evolution towards a parasitic or pathogen life style.

The ability to parasitize or manipulate hosts has emerged multiple times independently during evolution not only between different kingdoms (e.g. arthropods, nematodes, fungi, oomycetes) but also multiple times within a same kingdom. At several occasions this has concerned species interacting negatively (parasites and pathogens) or indirectly in a postive manner (biocontrol agents) with plant health. Omics data now cover species with different lifestyles in these kingdoms including parasites, pathogens and free-living ones. This constitutes an important resource to perform comparative genomics analyses enabling the identification of singularities shared between different species having evolved a same life style in a convergent manner. Hence, genomic signatures of convergent and parallel evolution towards a parasitic or pathogenic life can be identified. This kind of research can inform on evolutionary innovations at the genome level essential to adaptation towards these life styles. The events under consideration most likely took place at geological scales.

Translational perspectives

Identification of genetic novelties or genomic singularities common to different species having evolved a parasitic or pathogenic life style. The corresponding genes probably play key central roles in the ability of these species to parasitize and manipulate their hosts. Targeting specifically these genes via reverse ecology approaches would allow altering the associated functions an thus contribute to the development of new methods to control plant pests and parasites.

Mechanisms of genomic plasticity contributing to the recent and contemporary adaptability of these species

At more contemporary scales, how do these same pathogen and parasite species evolve and adapt to environmental changes and even to the control methods deployed against some of them? The availability of omics data for different populations within the same species now allows us to explore genome plasticity and variability at shorter time scales. Comparing omics data from different populations with a reference genome of the same species allows us to identify point mutations and structural variations in these genomes. These same data also allow the identification of genes under diversifying selection pressure probably related to recent adaptations vs. those under purifying selection pressure. Similarly, this opens the way to the identification of essential core genes that are universally conserved between different populations vs. "dispensable" genes whose presence/absence varies according to the populations and possibly their biological or ecological traits.

Translational perspectives

Identification of key genes involved in the adaptation of pests and pathogens to new hosts or environment as well as in the resistance to control methods eventually deployed against them. Here again, reverse ecology approaches targeting these genes and their functions could help in the development of new control methods against crop pests or optimize the chances of success of biocontrol agents.

Main study models

The GAME team is mainly interested in the genomes of parasites and pathogens that negatively affect plant health as well as those of biocontrol agents deployed against crop pests. The models studied at Institut Sophia Agrobiotech are of course the focus of our genomic analyses.

Plant parasites and pathogens:

Plant parasitic nematodes

Along with arthropods, nematodes are the most abundant and diverse animals on our planet. These worms, mostly smaller than 1 mm, are found in almost every environment on earth. In nematodes, the ability to parasitize plants has emerged at least four times independently during evolution. About 100 nematode genomes are publicly available, of which about 15 are plant parasites. Displaying diverse modes of parasitism including ecto- vs. endo-parasitic species as well as sedentary vs. migratory species, this phylum is a perfect model to study the genomic signatures of adaptation to plant parasitism. Our research in this field is conducted in coordination with the IPN team and international collaborators.

Phytopathogenic oomycetes

Oomycetes are filamentous eukaryotic organisms phylogenetically distant from fungi, plants or animals. They belong to the Stramenopiles clade which also contains the brown algae. In the phylogeny of these organisms, a phytopathogenic lifestyle has emerged several times independently during evolution. Genomes are publicly available for nearly 100 species, including about ten phytopathogens. Again, these multiple and independent adaptations open the possibility of identifying signatures of adaptation to a plant pathogenic lifestyle. Our research in this field is conducted in coordination with the team IPO.

Phytophagous arthropods

Arthropods are one of if not the most evolutionarily successful phylum in the animal world. Genomic data are available for hundreds and soon thousands of species including multiple phytophagous or plant parasitic species representing multiple and independent evolutions of this way of life. This phylum rich in high quality genomes and for which a dated phylogeny is available paves the way for comparative analyses associated with a molecular clock enabling the identification of significant expansions/reductions of gene families related to adaptation to different life styles. On these models, our research will be conducted in coordination with international partners and the ID, M2P2 and BPI teams.

Biocontrol agents:

Parasitoid wasps of the genus Trichogramma

Miniature wasps of the genus Trichogramma, generally < 1 mm in size, are oophagous parasitoids. This means that the larvae of these wasps develop inside the eggs of host insects at their expense. Thanks to this ability, different Trichogramma species are used in biological control to manage populations of insect pests of crops. Genomic data are available for less than 10 species out of the 200 known in this genus. However, thanks to the Trichogramma species collection EP-Coll, located in our host laboratory, a unique resource for sequencing new genomes is locally available. Moreover,RDLB and M2P2 teams have been generating rich biological and phenotypic characterization data that will be highly interesting to connect with genome plasticity data.

Originality of our team

By studying different species models, including phylogenetically distant phyla, and by integrating multi-omics data, the GAME team aims to obtain an integrative vision of the mechanisms of genomic plasticity linked to the adaptive evolution of parasites and pathogens and thus significantly advance knowledge in this field.

Furthermore, by taking into account the gene pool present in the natural environment of these species, we wish to extend the concept of holobiont to that of hologenome and thus learn more about the genetic flows between species in the same environment.