Comparative, population and functional genomics of Tenebrio

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

Comparative, population and functional genomics of Copepods

Copepods are crustaceans and the most abundant animal on Earth.

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.

Computational Biology and Bioinformatic Tools Development

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.

Team members

Sana Haddad
Bioinformatics engineer

Dr. Leonardo Panunzi
Computational Biologist Researcher

Dr. Kevin Sugier
Post-doctoral fellow in copepod genomics

Dr. Amin Madoui
Molecular and Computational Biologist
Group leader

Lucas Rocha Ferreira
PhD student in quantitative genomics

Former members

Alexis Culpin
Master student in bioinformatician in 2023

Evangelia Eleftheriou
Bioinformatician from 2019 to 2022

Dr. Romuald Laso-Jadart
PhD student from 2018 to 2020

Loïc Dorval
Master student in bioinformatics 2021

Théo Frézouls
Master student in bioinformatics 2021

Soheib Kerbache
Bioinformatician from 2018-2019

Majda Arif
Bioinformatician from 2017-2019

Latest Team Publications

2023

Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations. Laso-Jadart R, O’Malley M, Sykulski AM, Ambroise C, Madoui MA BMC Ecolology and Evolution 23, 46 (2023). https://doi.org/10.1186/s12862-023-02160-8

Tenebrio molitor genomic structure among available populations. Eleftheriou E, Vacherie B, Labadie K, Athanassiou CG, Rigaud T, Moret Y, Lefebvre T, Madoui MA Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP), 2023; 2549-2551 doi: https://doi.org/10.3920/978-90-8686-940-4_616

Copepods' True Colors: Astaxanthin Pigmentation as an Indicator of Fitness. Vilgrain L, Maps F, Basedow S, Trudnowska E, Madoui MA, Niehoff B, Ayata SD. 2023. Ecosphere 14(6): e4489. https://doi.org/10.1002/ecs2.4489

2022

Chromosome-scale assembly of the yellow mealworm genome. Eleftheriou E, Aury J, Vacherie B, Istace B, Belser C, Noel B, Moret Y, Rigaud T, Berro F, Gasparian S, Labadie-Bretheau K, Lefebvre T, Madoui MA. Open Research Europe 2021, 2022; 1:94 doi: https://doi.org/10.12688/openreseurope.13987.1

Whole-genome scanning reveals selection mechanisms in epipelagic Chaetoceros diatom populations. Nef C, Madoui MA, Pelletier E, Bowler C. Plos Biology, 20(11): e3001893. https://doi.org/10.1371/journal.pbio.3001893

Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea. Da Silva O, Ayata SD, Ser-Giacomi E, Leconte J, Pelletier E, Fauvelot C, Madoui MA, Guidi L, Lombard F, Bittner L. Environmental Microbiology, 2022; 1– 14 doi: https://doi.org/10.1111/1462-2920.16171

2021

Male differentiation in the marine copepod Oithona nana reveals the development of a new nervous ganglion linked to Lin12-Notch-Repeat protein-associated proteolysis . Sugier K, Laso-Jadart R, Kerbache S, Kafer J, Arif M, Bertrand L, Labadie K, Martins N, Orvain C, Petit E, Poulain J, Vacherie B, Wincker P, Jamet JL, Alberti A, Madoui MA. Biology. 2021; 10(7):657. https://doi.org/10.3390/biology10070657

Estimating the travel time and the most likely path from Lagrangian drifters. O'Malley M, Sykulski AM, Laso-Jadart R, Madoui MA. Journal of Atmospheric and Oceanic Technology, 2022; 38(5), 1059-1073, doi: https://doi.org/10.1175/JTECH-D-20-0134.1

The first AI-based mobile application for antibiotic resistance testing. Pascucci M, Royer G, Adamek J, Aristizabal D, Blanche L, Bezzarga A, Boissinot D, Boniface-Chang G, Brunner A, Curel C, Dulac-Arnold G, Malou N, Nordon C, Runge V, Samson F, Sebastian E, Soukieh D, Vert JP, Ambroise C, Madoui MA. 2021. Nature Communications 12, 1173 (2021). https://doi.org/10.1038/s41467-021-21187-3.

2020
metaVaR: introducing metavariant species models for reference-free metagenomic-based population genomics. Laso-Jadart R, Ambroise C, Peterlongo P, Madoui MA. Plos One. 2020. e0244637. https://doi.org/10.1371/journal.pone.0244637

Investigating Population-scale Allele Specific Expression in Wild Populations of Oithona similis (Cyclopoida, Claus 1866). Laso-Jadart R, Sugier K, Petit E, Labadie K, Peterlongo P, Ambroise C, Wincker P, Jamet JL, Madoui MA. Ecology and Evolution. 2020; 10: 8894– 8905

2019
Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea. Arif M, Gauthier J, Sugier K, Iudicone D, Jaillon O, Wincker P, Peterlongo P, Madoui MA. Molecular Ecology Resources. 2019 Mar;19(2):526-535

Reference genome for pea provides insight into legume genome evolution. Kreplak J, Madoui MA, Cápal P, Novák P, Labadie K, Aubert G, Bayer PE, Gali KK, Syme RA, Main D, Klein A, Bérard A, Vrbová I, Fournier C, d'Agata L, Belser C, Berrabah W, Toegelová H, Milec Z, Vrána J, Lee H, Kougbeadjo A, Térézol M, Huneau C, Turo CJ, Mohellibi N, Neumann P, Falque M, Gallardo K, McGee R, Tar'an B, Bendahmane A, Aury JM, Batley J, Le Paslier MC, Ellis N, Warkentin TD, Coyne CJ, Salse J, Edwards D, Lichtenzveig J, Macas J, Doležel J, Wincker P, Burstin J. A Nat Genet. 2019 Sep;51(9):1411-1422. doi: 10.1038/s41588-019-0480-1. Epub 2019 Sep 2. PMID: 31477930.

2018

Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy. Sugier K, Vacherie B, Cornils A, Wincker P, Jamet JL, Madoui MA. PeerJ. 2018 May 14;6:e4685.

A global ocean atlas of eukaryotic genes. Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P. Nature Communications. 2018 Jan 25;9(1):373.

2017

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona. Madoui MA, Poulain J, Sugier K, Wessner M, Noel B, Berline L, Labadie K, Cornils A, Blanco-Bercial L, Stemmann L, Jamet JL, Wincker P. Molecular Ecology. 2017 Sep;26(17):4467-4482.