Section: Partnerships and Cooperations

National Initiatives

ANR

Project HydroGen: Metagenomic applied to ocean life study

Participants : Dominique Lavenier, Pierre Peterlongo, Claire Lemaitre.

Coordinator: P. Peterlongo (Inria/Irisa, GenScale, Rennes)

Duration: 42 months (Nov. 2014 – Apr. 2018)

Partners: CEA (Genoscope, Evry), INRA (AgroParisTech, Paris – MIG, Jouy-en-Jossas).

The HydroGen project aims to design new statistical and computational tools to measure and analyze biodiversity through comparative metagenomic approaches. The support application is the study of ocean biodiversity based on the analysis of seawater samples available from the Tara Oceans expedition.

Project SpeCrep: speciation processes in butterflies

Participants : Dominique Lavenier, Jeremy Gauthier, Fabrice Legeai, Claire Lemaitre, Pierre Peterlongo.

Coordinator: M. Elias (Museum National d'Histoire Naturelle, Institut de Systématique et d'Evolution de la Biodiversité, Paris)

Duration: 48 months (Jan. 2015 – Dec. 2018)

Partners: MNHN (Paris), INRA (Versailles-Grignon), Genscale Inria/IRISA Rennes.

The SpeCrep project aims at better understanding the speciation processes, in particular by comparing natural replicates from several butterfly species in a suture zone system. GenScale’s task is to develop new efficient methods for the assembly of reference genomes and the evaluation of the genetic diversity in several butterfly populations.

Project Supergene: The consequences of supergene evolution.

Participants : Dominique Lavenier, Fabrice Legeai, Claire Lemaitre, Pierre Peterlongo.

Coordinator: M. Joron (Centre d'Ecologie Fonctionnelle et Evolutive (CEFE) UMR CNRS 5175, Montpellier)

Duration: 48 months (Nov. 2018 – Oct. 2022)

Partners: CEFE (Montpellier), MNHN (Paris), Genscale Inria/IRISA Rennes.

The Supergene project aims at better understanding the contributions of chromosomal rearrangements to adaptive evolution. Using the supergene controlling adaptive mimicry in a polymorphic, ubiquitous butterfly from the Amazon basin (H. numata), the project will investigate the evolution of inversions involved in adaptive polymorphism and their consequences on population biology. GenScale’s task is to develop new efficient methods for the detection and genotyping of inversion polymorphism with several types of re-sequencing data.

PIA: Programme Investissement d’Avenir

RAPSODYN: Optimization of the rapeseed oil content under low nitrogen

Participants : Dominique Lavenier, Claire Lemaitre, Sebastien Letort, Pierre Peterlongo, Guendal Virlet.

Coordinator: N. Nesi (Inra, IGEPP, Rennes)

Duration: 99 months (2012-2020)

Partners: 5 companies, 9 academic research labs.

The objective of the Rapsodyn project is the optimization of the rapeseed oil content and yield under low nitrogen input. GenScale is involved in the bioinformatics work package to elaborate advanced tools dedicated to polymorphism and application to the rapeseed plant. (http://www.rapsodyn.fr)

Programs from research institutions

Inria Project Lab: Neuromarkers

Participants : Dominique Lavenier, Pierre Peterlongo, Claire Lemaitre, Celine Le Beguec.

Coordinator: O. Colliot (Inria, Aramis, Paris)

Duration: 4 years (2017-2020)

Partners: Inria (Aramis, Bonsai, Dyliss, GenScale, XPOP), ICM

The IPL Neuromarkers aims to design imaging bio-markers of neuro-degenerative diseases for clinical trials and study of their genetic associations. In this project, GenScale bring its expertise in the genomics field. More precisely, given a case-control population, a first step is to locate small genetic variations (SNPs, small indels) from their genomes. Then, having these variations together with brain images (also partitioned into case-control data sets), the challenge is to select variants that present potential correlation with brain images.