Section: Partnerships and Cooperations

National Initiatives

ANR

Project HydroGen: Metagenomics 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. 2019)

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 generated by the Tara Oceans expedition.

Project SpeCrep: speciation processes in butterflies

Participants : Dominique Lavenier, 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 – Jul. 2019)

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 : Anne Guichard, 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 locus controlling adaptive mimicry in a polymorphic 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.

Project SeqDigger: Search engine for genomic sequencing data

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo.

Coordinator: P. Peterlongo

Duration: 48 months (jan. 2020 – Dec. 2024)

Partners: Genscale Inria/IRISA Rennes, CEA genoscpoe, MIO Marseille, Institut Pasteur Paris

https://www.cesgo.org/seqdigger/

The central objective of the SeqDigger project is to provide an ultra fast and user-friendly search engine that compares a query sequence, typically a read or a gene (or a small set of such sequences), against the exhaustive set of all available data corresponding to one or several large-scale metagenomic sequencing project(s), such as New York City metagenome, Human Microbiome Projects (HMP or MetaHIT), Tara Oceans project, Airborne Environment, etc. This would be the first ever occurrence of such a comprehensive tool, and would strongly benefit the scientific community, from environmental genomics to biomedicine.

PIA: Programme Investissement d’Avenir

RAPSODYN: Optimization of the rapeseed oil content under low nitrogen

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo, Gwendal 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 detection and their application to the rapeseed plant. (http://www.rapsodyn.fr)

Programs from research institutions

Inria Project Lab: Neuromarkers

Participants : Dominique Lavenier, Pierre Peterlongo, Claire Lemaitre, Céline Le Beguec, Téo Lemane.

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

Duration: 4 years (2017-2020)

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

The Neuromarkers IPL aims to design imaging bio-markers of neuro-degenerative diseases for clinical trials and study of their genetic associations. In this project, GenScale brings its expertise in the genomics field. More precisely, given a case-control population, a first step is to identify small genetic variations (SNPs, small indels) from their genomes. Then, using 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.