The mealworm Tenebrio molitor is a beetle becoming intensively used in farming as a protein-rich animal feed.
How the team is involved in the world feeding challenge? We build the T. molitor genome using the last NGS technologies allowing a chromosome-scale assembly of the genome.
How to use genomics to improve Tenebrio farming? We analyse T. molitor molecular diversity and use NGS to genotype and develop innovative genomic projects for efficient breeding of new strains for industrial farming.
How can we better understand Tenebrio molecular immune response? We decipher T. molitor signaling pahways involved in immune response by integrating protein-protein interaction, RNAi and immunofluorescence.
Collaboration: We collaborate with French Tenebrio experts and researchers Dr. Yannick Morret from CNRS, Pr. Thierry Rigaut from University of Burgundy and Dr. Thomas Lefebvre from Ynsect.
This work is done in collaboration with Ynsect and currently funded by the H2020 FARMYNG, YnFabre BPI France and ANR OPTIM-INSECT grants
How physico-chemical conditions and marine currents shape copepod genome evolution? We identify the main environmental factors driving population genomic differentiation and gene flow for dozens of copepods species. In this endeavor, we applied in-house computational methods on large-scale metagenomic and metatranscriptomic data from the Tara Oceans expeditions.
What are the copepod genes and biological processes under natural selection? We infer the impact of nucleotidic polymorphism under selection on the copepod biology with a focus on nervous system and lipid metabolism.
Is there a link between natural selection and allele specific expression? The link between allele-specific expression and natural selection is studied by identifying genes that are targeted by both mechanisms by combining genomics and transcriptomics.
Collaboration: We collaborate with copepodologists, marine biologists and oceanographers, Dr. Sakina Ayata from Sorbonne University, Pr. Frederic Maps from Laval University, Dr. Leocadio Blanco-Bercial from the Bermuda Institute of Ocean Sciences and Dr. Astrid Cornils from the Alfred Wegener Institute.
We develop new computational approaches and pipelines to adress multi-omics data integration challenges.
How to deal with the lack of reference genomes? We developed metaVaR, R package for reference-free metagenomic-based population genomics.
How to combine metatranscriptomic and metagenomic data for variant calling? We developed psADE, a statistical framework to estimate allele-specific expression from metagenomics and metatranscriptomics data.
How to know if our haplotype reconstruction is correct? We developed HaploSim for simulating and analysing haplotypes built from pooled-individuals data.
Collaboration: We collaborate with the precious statistician Pr. Christophe Ambroise from the University of Paris-Saclay and the devoted informatician Dr. Pierre Peterlongo from the Inria of Rennes.
Interested in doing a PhD, a post-doc or a master internship? If you like this team , genomics and challenges, please submit your resume
18 Route du Panorama, 92 260 Fontenay-aux-Roses, France
mohammedamin.madoui@cea.fr
@transpositional