GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Duret Laurent

Directeur de recherche

CNRS

Address: 69622 VILLEURBANNE cedex
69622 VILLEURBANNE cedex

Tel: 33 04 72 44 62 97

Email

Batiment Mendel 2eme étage. Bureau 12.025

Genomes are the product of various evolutionary processes: certain genomic traits that we observe today reflect functional constraints that currently operate or that have operated in the past; others result from non-adaptive processes. To identify the features of the genome that are important for its functioning, it is necessary to look for features whose mode of evolution deviates from the neutralist model: this is the basic principle of the comparative analysis of genomes, which is at the heart of all my research activity. My work follows a double logic: study the evolution of genomes to better understand how they work - and vice versa, take into account the molecular mechanisms of genome functioning in order to better interpret sequence evolution. We explore genetic diversity at different level, both across species and within species (population genomics). My work is based on bioinformatic and statistical analysis of sequences, but also relies heavily on close collaborations with ‘wet-lab' biologists.
These last years, my main focus has been on exploring the consequences of homologous recombination on genome evolution. In particular, we have discovered that in many species, recombination induces non-Mendelien inheritance, favoring the fixation of GC-alleles (gBGC – for GC-Biased Gene Conversion). This non-adaptive process has a major impact on the evolution of genomic landscapes and also on gene expression processes. We are now trying to understand how and why does gBGC evolve, and how and why do recombination rates vary in space (along chromosomes) and in time (across species).
I am also interested in understanding how the constraints imposed by the cost of gene expression shape genome evolution. We have shown that gene expression level is an important determinant of selective pressures acting on numerous features: on protein sequences, on gene dosage, on splicing accuracy, and on translation efficiency. We are now exploring how variation in the efficacy of selection contributes to the evolution of the complexity of gene expression patterns across species.
I am also working, in collaboration with researchers from Paris and Gif, on the genomics of Paramecia. This unicellular eukaryote displays many very peculiar features that make it a fantastic model to explore  various topics (whole genome duplications, proliferation of selfish genetic elements, alternative splicing, transgenerational inheritance of epigenetic modifications, …).

 

Publications

Display of 1 to 30 publications on 171 in total

Prevalence of PRDM9-dependent vs PRDM9-independent recombination hotspots in animals

Laurent Duret

RecomBern .

Conference paper

see the publication

GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes

Florian Bénitière, Laurent Duret, Anamaria Necsulea

NAR Genomics and Bioinformatics . 6 ( 2 ) : lqae064

DOI: 10.1093/nargab/lqae064

Journal article

see the publication

High prevalence of PRDM9-independent recombination hotspots in placental mammals

Julien Joseph, Djivan Prentout, Alexandre Laverré, Théo Tricou, Laurent Duret

Proceedings of the National Academy of Sciences of the United States of America . 121 ( 23 ) : e2401973121

DOI: 10.1073/pnas.2401973121

Journal article

see the publication

PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids

Marie Raynaud, Paola Sanna, Julien Joseph, Julie A. J. Clément, Yukiko Imai, Jean-Jacques Lareyre...

DOI: 10.1101/2024.03.06.583651

Preprint

see the publication

Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans

Florian Bénitière, Anamaria Necsulea, Laurent Duret

eLife . 13 : RP93629

DOI: 10.7554/eLife.93629.3

Journal article

see the publication

Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis : a model based exploration of the PRDM9 intra-genomic Red Queen

Alice Genestier, Laurent Duret, Nicolas Lartillot

PLoS Genetics . 20 ( 5 ) : e1011274

DOI: 10.1371/journal.pgen.1011274

Journal article

see the publication

Population designations in biomedical research: limitations and perspectives

Caroline Gombault, Guillaume Grenet, Laure Ségurel, Laurent Duret, François Gueyffier, Pascal Cathébras...

HLA: Immune Response Genetics . 101 ( 1 ) : 3-15

DOI: 10.1111/tan.14852

Journal article

see the publication

Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Diamantis Sellis, Frédéric Guérin, Olivier Arnaiz, Walker Pett, Emmanuelle Lerat, Nicole Boggetto...

PLoS Biology . 19 ( 7 ) : e3001309

DOI: 10.1371/journal.pbio.3001309

Journal article

see the publication

DILS: Demographic inferences with linked selection by using ABC

Christelle Fraïsse, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stephane Delmotte, Jonathan Romiguier...

Molecular Ecology Resources .

DOI: 10.1111/1755-0998.13323

Journal article

see the publication

Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

Natalia Sawka-Gądek, Alexey Potekhin, Deepankar Pratap Singh, Inessa Grevtseva, Olivier Arnaiz, Simon Penel...

Genome Biology and Evolution . ( evaa258 )

DOI: 10.1093/gbe/evaa258

Journal article

see the publication

How consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?

Marie Cariou, Hélène Henri, Sonia Martinez, Laurent Duret, Sylvain Charlat

Molecular Ecology Resources . 20 ( 5 ) : 1294-1298

DOI: 10.1111/1755-0998.13178

Journal article

see the publication

Bedrock radioactivity influences the rate and spectrum of mutation

Nathanaëlle Saclier, Patrick Chardon, Florian Malard, Lara Konecny-Dupré, David Eme, Arnaud Bellec...

eLife . 9 : e56830

DOI: 10.7554/eLife.56830

Journal article

see the publication

Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot

Daphné Reiss, Gladys Mialdea, Vincent Miele, Damien M. de Vienne, Jean Peccoud, Clément Gilbert...

PLoS Genetics . 15 ( 2 ) : e1007965

DOI: 10.1371/journal.pgen.1007965

Journal article

see the publication

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren, Carina Mugal

Genome Biology . 20 ( 1 )

DOI: 10.1186/s13059-018-1613-z

Journal article

see the publication

Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints

Florian Massip, Marc Laurent, Caroline Brossas, José miguel Fernández-Justel, Maria Gomez, Marie-Noëlle Prioleau...

Nucleic Acids Research . 47 ( 10 ) : 5114-5125

DOI: 10.1093/nar/gkz182

Journal article

see the publication

Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest

Georgios Koutsovoulos, Eder Marques, Marie Jeanne Arguel, Laurent Duret, Andressa C. Z. Machado, Regina M. D. G. Carneiro...

Evolutionary Applications . 13 : 1-16

DOI: 10.1111/eva.12881

Journal article

see the publication

Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

Laurent Guéguen, Laurent Duret

Molecular Biology and Evolution . 35 ( 3 ) : 734-742

DOI: 10.1093/molbev/msx308

Journal article

see the publication

PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites

Boubou Diagouraga, Julie Clément, L. Duret, Jan Kadlec, Bernard de Massy, Frédéric Baudat

Molecular Cell . 69 ( 5 ) : 853 - 865.e6

DOI: 10.1016/j.molcel.2018.01.033

Journal article

see the publication

Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

Nicolas Galtier, Camille Roux, Marjolaine Rousselle, Jonathan Romiguier, Emeric Figuet, Sylvain Glemin...

Molecular Biology and Evolution . 35 ( 5 ) : 1092 - 1103

DOI: 10.1093/molbev/msy015

Journal article

see the publication

Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

Nathanaëlle Saclier, Clémentine François, Lara Konecny-Dupré, Nicolas Lartillot, Laurent Guéguen, L. Duret...

Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912

DOI: 10.1093/molbev/msy184

Journal article

see the publication

The Red Queen model of recombination hot-spot evolution: a theoretical investigation

Thibault Latrille, L. Duret, Nicolas Lartillot

Philosophical Transactions of the Royal Society B: Biological Sciences .

DOI: 10.1098/rstb.2016.0463

Journal article

see the publication

The global impact of Wolbachia on mitochondrial diversity and evolution

Marie Cariou, Laurent Duret, Sylvain Charlat

Journal of Evolutionary Biology . 30 ( 12 ) : 2204-2210

DOI: 10.1111/jeb.13186

Journal article

see the publication

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

C Grey, Julie a J Clément, J Buard, B Leblanc, I Gut, M Gut...

Genome Research . 27 ( 4 ) : 580-590

DOI: 10.1101/gr.217240.116

Journal article

see the publication

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Baptiste Saudemont, Alexandra Popa, Joanna Parmley, Vincent Rocher, Corinne Blugeon, Anamaria Necsulea...

Genome Biology . 18 : 208

DOI: 10.1186/s13059-017-1344-6

Journal article

see the publication

Less effective selection leads to larger genomes

Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen...

Genome Research . 27 : 1016-1028

DOI: 10.1101/gr.212589.116

Journal article

see the publication

No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes

Clémentine François, L. Duret, Laurent Simon, Florian Mermillod-Blondin, Florian Malard, Lara Konecny-Dupré...

Molecular Biology and Evolution . 33 ( 10 ) : 2605–2620

DOI: 10.1093/molbev/msw131

Journal article

see the publication

GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

Florent Lassalle, Séverine Périan, Thomas Bataillon, Xavier Nesme, L. Duret, Vincent Daubin

PLoS Genetics . 11 ( 2 ) : 1-20

DOI: 10.1371/journal.pgen.1004941

Journal article

see the publication