ANCESTROME - Approche de phylogénie intégrative pour la reconstruction de "-omes" ancestraux


Fiche  technique du Projet

• Programme : Investissements d’Avenir – Action BioInformatique  - ANR 2010
• Coordinateur: Université Claude Bernard Lyon 1, Vincent DAUBIN
• Partenaires :
o Université Claude Bernard Lyon 1
o CNRS
o Université Montpellier 2
o ENS Lyon
o Institut Pasteur

• Coût Total: 8 267 724 €
• Contribution ANR : 2 200 000 €
• Durée : 2012 - 2016
• Site web: http://ancestrome.univ-lyon1.fr/

Context / Contexte

Ancestrome is a research project that aims to study genome organization and functioning of extant living organisms to build integrative models to reconstruct evolutionary intermediates together with the evolutionary processes that have generated them.
It is funded by the ANR agency on the Bioinformatics “Investissements d’Avenir” call.
A critical step in the development of methods to reconstruct the evolution of genomes is the modeling of the processes that relate gene phylogenies to species phylogenies. We have developed methods for integrating events of gene duplication, gene loss and lateral gene transfer in the simultaneous reconstruction of species and gene histories. These methods yield much better estimates of the gene content of ancestral genome, and hence open the door to accurate reconstructions of ancestral species characteristics. This includes cellular and genome organizations, or metabolic capabilities as deduced from genome content, but also virtually any internal or external factors that have left a trace in the genomic record, such as the environment to which the species has adapted, its resources, parasites or demography.

Objectives / objectifs

The main objectives of this proposal are the following:
(1) Modeling the processes of gene evolution and co-evolution with the aid of High Performance Computing
(2) Reconstructing ancestral genomes with functional dependencies
(3) Impact of phylogeny algorithmics: developing a probabilistic framework that integrates gene descent and gene dependence
(4) Create a community effort between evolutionary biology and computer science

The scientific program is organized with the following work-packages:
- WP 1: Phylogenetic reconstruction of genomes history,
- WP 2: Gene co-evolution
- WP 3: Ancestral chromosome organization
- WP 4: Ancestral metabolic networks
- WP 5: Ancestral protein complexes
- WP 6: Ancestral environments and ecology
- WP 7: Data management and valorization 

Rôle de LIP

LIP a accompagné le projet dans sa phase de montage : définition des attendus du financeur, montage administratif et financier du projet, conseil à la rédaction.
LIP accompagne également ce projet dans son management administratif et financier.