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 61 to 90 publications on 173 in total

Detecting positive selection within genomes: the problem of biased gene conversion

A. Ratnakumar, Sylvain Mousset, S. Glémin, J. Berglund, N. Galtier, L. Duret...

Philosophical Transactions of the Royal Society B: Biological Sciences . 365 ( 1552 ) : 2571-2580

DOI: 10.1098/rstb.2010.0007

2010

Journal article

see the publication

Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

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

Emerging Model Organisms . 2010 : 1-55

2010

Journal article

see the publication

The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution

Jean-François Gout, Daniel Kahn, Laurent Duret

PLoS Genetics . 6 ( 5 ) : e1000944

DOI: 10.1371/journal.pgen.1000944

2010

Journal article

see the publication

Mutation Patterns in the Human Genome:More Variable Than Expected

L. Duret

PLoS Biology . 7(2) e1000028 : 803-806

2009

Journal article

see the publication

Monoallelic expression and tissue specificity are associated with high crossover rates

A. Necşulea, M. Sémon, L. Duret, L.D. Hurst

Trends in Genetics . 25(12) : 519-522

2009

Journal article

see the publication

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

N. Galtier, L. Duret, S. Glémin, Vincent Ranwez

Trends in Genetics . 25(1) : 1-5

2009

Journal article

see the publication

The relationship between DNA replication and human genome organization.

Anamaria Necsulea, Claire Guillet, Jean-Charles Cadoret, Marie-Noëlle Prioleau, L. Duret

Molecular Biology and Evolution . 26 ( 4 ) : 729-741

DOI: 10.1093/molbev/msn303

2009

Journal article

see the publication

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

L. Duret, N. Galtier

Annual Review of Genomics and Human Genetics . 10 : 285-311

2009

Journal article

see the publication

L’évolution des chromosomes sexuels humains

Gabriel Marais, L. Duret

Biofutur . 304 : 40-41

2009

Journal article

see the publication

N. Galtier, L. Duret

incollection . -- : 273-277

2008

Journal article

see the publication

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline.

L. Duret, Jean Cohen, Claire Jubin, Philippe Dessen, Jean-François Goût, Sylvain Mousset...

Genome Research . 18 ( 4 ) : 585-96

DOI: 10.1101/gr.074534.107

2008

Journal article

see the publication

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

A. Studer, Simon Penel, L. Duret, M. Robinson-Rechavi

Genome Research . 18 : 1393-1402

2008

Journal article

see the publication

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

L. Duret, P.F. Arndt

PLoS Genetics . 4 : 1-19

2008

Journal article

see the publication

C. Keime, M. Sémon, Dominique Mouchiroud, L. Duret, Olivier Gandrillon

BMC Bioinformatics . 8 : 1-11

2007

Journal article

see the publication

Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution

Nicolas Galtier, L. Duret

Trends in Genetics . 23 ( 6 ) : 273-277

DOI: 10.1016/j.tig.2007.03.011

2007

Journal article

see the publication

Unexpected observations after mapping LongSAGE tags to the human genome.

Céline Keime, Marie Sémon, Dominique Mouchiroud, Laurent Duret, Olivier Gandrillon

BMC Bioinformatics . 8 : 154

DOI: 10.1186/1471-2105-8-154

2007

Journal article

see the publication

Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies.

Karine Buchet-Poyau, Julien Courchet, Hervé Le Hir, Bertrand Séraphin, Jean-Yves Scoazec, L. Duret...

Nucleic Acids Research . 35 ( 4 ) : 1289-300

DOI: 10.1093/nar/gkm016

2007

Journal article

see the publication

Insights into social insects from the genome of the honeybee Apis mellifera

G.M. Weinstock, G.E. Robinson, R.A. Gibbs, K.C. Worley, J.D. Evans, R. Maleszka...

Nature . 443 : 931-949

2006

Journal article

see the publication

GC Content Evolution of the Human and Mouse Genomes : Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates.

A. Khelifi, J. Meunier, L. Duret, Dominique Mouchiroud

Journal of Molecular Evolution . 62 : 745-752

2006

Journal article

see the publication

Global trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia

Jean-Marc Aury, Olivier Jaillon, * Laurent Duret, Benjamin Noel, Claire Jubin, Betina M. Porcel...

Nature . 444 ( 7116 ) : 171-178

DOI: 10.1038/nature05230

2006

Journal article

see the publication

The GC Content of Primates and Rodents Genomes Is Not at Equilibrium : a Reply to Antezana

L. Duret

Journal of Molecular Evolution . -- : 803-806

2006

Journal article

see the publication

No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

M. Sémon, J.R. Lobry, L. Duret

Molecular Biology and Evolution . 23 : 523-529

2006

Journal article

see the publication

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

Publications

Detecting positive selection within genomes: the problem of biased gene conversion

Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution

Mutation Patterns in the Human Genome:More Variable Than Expected

Monoallelic expression and tissue specificity are associated with high crossover rates

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

The relationship between DNA replication and human genome organization.

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

L’évolution des chromosomes sexuels humains

Comment on “Human-Specific Gain of Function in a Developmental Enhancer”

Differential retention of metabolic genes following whole-genome duplication

Databases of Homologous Gene Families for Comparative Genomics

ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in Ribosome biogenesis.

Translational control of intron splicing in eukaryotes

Biased Gene Conversion and its Impact on Human Genome Evolution

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline.

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

Neutral Theory: The Null Hypothesis of Molecular Evolution

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline

Genome-wide studies highlight indirect links between human replication origins and gene regulation.

Unexpected observations after mapping LongSAGE tags to the human genome

Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution

Unexpected observations after mapping LongSAGE tags to the human genome.

Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies.

Insights into social insects from the genome of the honeybee Apis mellifera

GC Content Evolution of the Human and Mouse Genomes : Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates.

Global trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia

The GC Content of Primates and Rodents Genomes Is Not at Equilibrium : a Reply to Antezana

No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans