GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Duret Laurent

Directeur de recherche

CNRS

Address: 69622 VILLEURBANNE cedex
69622 VILLEURBANNE cedex

_{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 31 to 60 publications on 173 in total

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

2016

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

2015

Journal article

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Quantification of GC-biased gene conversion in the human genome

Sylvain Glemin, Peter F. Arndt, Messer W. Philip, Petrov M. Dmitri, Nicolas Galtier, L. Duret

Genome Research . 25 ( 8 ) : 1215 - 1228

DOI: 10.1101/gr.185488.114

2015

Journal article

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Optimization of multiplexed RADseq libraries using low-cost adaptors

Hélène Henri, Marie Cariou, Gabriel Terraz, Sonia Martinez, Adil El Filali, Marine Veyssière...

Genetica . 143 ( 2 ) : 139-143

DOI: 10.1007/s10709-015-9828-3

2015

Journal article

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Occurrence of a non deleterious gene conversion event in the BRCA1 gene

C. Tessereau, M. Leone, M. Buisson, L. Duret, O. M. Sinilnikova, S. Mazoyer

Genes, Chromosomes & Cancer . 54 : 646-52

DOI: 10.1002/gcc.22278

2015

Journal article

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Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing

C. Tessereau, Yann Lesecque, N. Monnet, M. Buisson, L. Barjhoux, M. Leone...

Nucleic Acids Research . 42 ( 14 ) : 9121-30

DOI: 10.1093/nar/gku639

2014

Journal article

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The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

Franck Picard, Jean-Charles Cadoret, Benjamin Audit, Alain Arneodo, Adriana A. Alberti, Christophe Battail...

PLoS Genetics . 10 ( 5 ) : e1004282

DOI: 10.1371/journal.pgen.1004282

2014

Journal article

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The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes

Y Lesecque, S. S. Glemin, N. Lartillot, D. Mouchiroud, L. Duret

PLoS Genetics . 10 : e1004790

DOI: 10.1371/journal.pgen.1004790

2014

Journal article

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Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome

E. M. Kvikstad, L. Duret

Molecular Biology and Evolution . 31 : 23-36

DOI: 10.1093/molbev/mst185

2014

Journal article

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Comparative population genomics in animals uncovers the determinants of genetic diversity

Jonathan Romiguier, P Gayral, M Ballenghien, Arnaud Bernard, V Cahais, Anne Chenuil...

Nature . 515 ( 7526 ) : 261-263

DOI: 10.1038/nature13685

2014

Journal article

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GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance

Y. Lesecque, D. Mouchiroud, L. Duret

Molecular Biology and Evolution . 30 : 1409--19

DOI: 10.1093/molbev/mst056

2013

Journal article

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XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

C. Vallot, C. Huret, Yann Lesecque, A. Resch, N. Oudrhiri, A. Bennaceur-Griscelli...

Nature Genetics . 45 : 239--41

DOI: 10.1038/ng.2530

2013

Journal article

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The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

S. B. Montgomery, D. L. Goode, E. Kvikstad, C. A. Albers, Z. D. Zhang, X. J. Mu...

Genome Research . 23 : 749--61

DOI: 10.1101/gr.148718.112

2013

Journal article

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Eloge de l'ADN poubelle

Laurent Duret, Sylvain Charlat

Pour la science . 81 : 10--17

2013

Journal article

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Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

Marie Cariou, Laurent Duret, Sylvain Charlat

Ecology and Evolution . 3 ( 4 ) : 846-852

DOI: 10.1002/ece3.512

2013

Journal article

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Genome-scale coestimation of species and gene trees.

Bastien Boussau, Gergely J Szöllosi, L. Duret, Manolo Gouy, Eric Tannier, Vincent Daubin

Genome Research . 23 ( 2 ) : 323-330

DOI: 10.1101/gr.141978.112

2013

Journal article

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XACT, a long non-coding transcript coating the active X chromosome in human pluripotent cells

Céline Vallot, Christophe Huret, Yann Lesecque, Alissa Resch, Noufϊssa Oudrhiri, Annelise Bennaceur...

Epigenetics and Chromatin: Interactions and processes . 6 ( Suppl 1 ) : O33

DOI: 10.1186/1756-8935-6-S1-O33

2013

Conference paper

see the publication

Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

Eugénie Pessia, Alexandra Popa, Sylvain Mousset, Clément Rezvoy, Laurent Duret, G. Marais

Genome Biology and Evolution . 4 : 787-794

DOI: 10.1093/gbe/evs052

2012

Journal article

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The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.

Olivier Arnaiz, Nathalie Mathy, Céline Baudry, Sophie Malinsky, Jean-Marc Aury, Cyril Denby Wilkes...

PLoS Genetics . 8 ( 10 ) : e1002984

DOI: 10.1371/journal.pgen.1002984

2012

Journal article

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High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, L. Duret

Bioinformatics . 28 ( 8 ) : 1078-85

DOI: 10.1093/bioinformatics/bts098

2012

Journal article

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Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes.

Brian P. Cusack, Peter F. Arndt, L. Duret, Hugues Roest Crollius

PLoS Genetics . 7 ( 10 ) : e1002276

DOI: 10.1371/journal.pgen.1002276

2011

Journal article

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Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

Corinne Chureau, Sophie Chantalat, Antonio Romito, Angélique Galvani, Laurent Duret, Philip Avner...

Human Molecular Genetics . 20 ( 4 ) : 705-718

DOI: 10.1093/hmg/ddq516

2011

Journal article

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Meiotic recombination favors the spreading of deleterious mutations in human populations

Anamaria Necsulea, L. Duret, Alexandra Popa, David N. Cooper, Peter Stentson, Dominique Mouchiroud...

Human Mutation . 32 ( 2 ) : 198-206

DOI: 10.1002/humu.21407

2011

Journal article

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Modélisation des systèmes biologiques, bioinformatique

Olivier Gascuel, P. Benas, C. Brun, D. Burnouf, Alexandre de Brevern, A. Denise...

Rapport de conjoncture 2010 du Comité national de la recherche scientifique . 978-2-271-07263-4 : chapitre 43, 845-858

2011

Book chapter

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Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

C. Chureau, S. Chantalat, A. Romito, A. Galvani, Laurent Duret, P. Avner...

Human Molecular Genetics . 20 : 705-718

DOI: 10.1093/hmg/ddq516

2011

Journal article

see the publication

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

T. Rouxel, J. Grandaubert, Jk. Hane, Claire Hoede, Angela P. van de Wouw, A. Couloux...

Nature Communications . 2 : 202

DOI: 10.1038/ncomms1189

2011

Journal article

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Ultra-fast sequence clustering from similarity networks with SiLiX

V. Miele, Simon Penel, L. Duret

BMC Bioinformatics . 12(116) : 1-9

DOI: 10.1186/1471-2105-12-116

2011

Journal article

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Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

J. Beisson, M. Bétermier, M.-H. Bré, J. Cohen, S. Duharcourt, L. Duret...

Emerging Model Organisms . 2010(1) : 1-55

2010

Journal article

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Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.

Olivier Arnaiz, Jean-François Goût, Mireille Bétermier, Khaled Bouhouche, Jean Cohen, L. Duret...

BMC Genomics . 11 ( 1 ) : 547

DOI: 10.1186/1471-2164-11-547

2010

Journal article

see the publication

Evolution Moléculaire

L. Duret, T. Bataillon, N. Bierne, Vincent Daubin, J. Dutheil, Christian Gautier...

Biologie évolutive . 978-2-8041-0161-9 : 114-173

2010

Book chapter

see the publication

Research Interests: "Nothing in a genome makes sense, except in the light of molecular evolution"...

Publications

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

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

Quantification of GC-biased gene conversion in the human genome

Optimization of multiplexed RADseq libraries using low-cost adaptors

Occurrence of a non deleterious gene conversion event in the BRCA1 gene

Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing

The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes

Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome

Comparative population genomics in animals uncovers the determinants of genetic diversity

GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance

XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

Eloge de l'ADN poubelle

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

Genome-scale coestimation of species and gene trees.

XACT, a long non-coding transcript coating the active X chromosome in human pluripotent cells

Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.

High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes.

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

Meiotic recombination favors the spreading of deleterious mutations in human populations

Modélisation des systèmes biologiques, bioinformatique

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Ultra-fast sequence clustering from similarity networks with SiLiX

Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.

Evolution Moléculaire