GECO Evolutionary and Computational Genomics
Bioinformatics, Phylogeny and Evolutionary Genomics Group
Duret Laurent
Directeur de recherche
CNRS
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 163 in total
The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes
PLoS Genetics . 10 : e1004790
Journal article
see the publicationStrong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome
Molecular Biology and Evolution . 31 : 23-36
Journal article
see the publicationComparative population genomics in animals uncovers the determinants of genetic diversity
Nature . 515 ( 7526 ) : 261-263
DOI: 10.1038/nature13685
Journal article
see the publicationIs RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization
Ecology and Evolution . 3 ( 4 ) : 846-852
DOI: 10.1002/ece3.512
Journal article
see the publicationGenome-scale coestimation of species and gene trees.
Genome Research . 23 ( 2 ) : 323-330
Journal article
see the publicationXACT, a long non-coding transcript coating the active X chromosome in human pluripotent cells
Epigenetics and Chromatin: Interactions and processes . 6 ( Suppl 1 ) : O33
Conference paper
see the publicationEvidence for Widespread GC-biased Gene Conversion in Eukaryotes
Genome Biology and Evolution . 4 : 787-794
DOI: 10.1093/gbe/evs052
Journal article
see the publicationThe Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.
PLoS Genetics . 8 ( 10 ) : e1002984
Journal article
see the publicationHigh-quality sequence clustering guided by network topology and multiple alignment likelihood.
Bioinformatics . 28 ( 8 ) : 1078-85
Journal article
see the publicationPreventing dangerous nonsense: selection for robustness to transcriptional error in human genes.
PLoS Genetics . 7 ( 10 ) : e1002276
Journal article
see the publicationFtx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region
Human Molecular Genetics . 20 ( 4 ) : 705-718
DOI: 10.1093/hmg/ddq516
Journal article
see the publicationMeiotic recombination favors the spreading of deleterious mutations in human populations
Human Mutation . 32 ( 2 ) : 198-206
DOI: 10.1002/humu.21407
Journal article
see the publicationModélisation des systèmes biologiques, bioinformatique
Rapport de conjoncture 2010 du Comité national de la recherche scientifique . 978-2-271-07263-4 : chapitre 43, 845-858
Book chapter
see the publicationUltra-fast sequence clustering from similarity networks with SiLiX
BMC Bioinformatics . 12(116) : 1-9
Journal article
see the publicationFtx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region
Human Molecular Genetics . 20 : 705-718
DOI: 10.1093/hmg/ddq516
Journal article
see the publicationEffector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
Nature Communications . 2 : 202
DOI: 10.1038/ncomms1189
Journal article
see the publicationParamecium tetraurelia: The Renaissance of an Early Unicellular Model
Emerging Model Organisms . 2010(1) : 1-55
Journal article
see the publicationGene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.
BMC Genomics . 11 ( 1 ) : 547
Journal article
see the publicationEvolution Moléculaire
Biologie évolutive . 978-2-8041-0161-9 : 114-173
Book chapter
see the publicationDetecting positive selection within genomes: the problem of biased gene conversion
Philosophical Transactions of the Royal Society B: Biological Sciences . 365 ( 1552 ) : 2571-2580
Journal article
see the publicationParamecium tetraurelia: The Renaissance of an Early Unicellular Model
Emerging Model Organisms . 2010 : 1-55
Journal article
see the publicationThe relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution
PLoS Genetics . 6 ( 5 ) : e1000944
Journal article
see the publicationMutation Patterns in the Human Genome:More Variable Than Expected
PLoS Biology . 7(2) e1000028 : 803-806
Journal article
see the publicationMonoallelic expression and tissue specificity are associated with high crossover rates
Trends in Genetics . 25(12) : 519-522
Journal article
see the publicationGC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates
Trends in Genetics . 25(1) : 1-5
Journal article
see the publicationThe relationship between DNA replication and human genome organization.
Molecular Biology and Evolution . 26 ( 4 ) : 729-741
Journal article
see the publicationComment on “Human-Specific Gain of Function in a Developmental Enhancer”
Science . 323(5915) : 714-715
Journal article
see the publicationBiased Gene Conversion and the Evolution of Mammalian Genomic Landscapes
Annual Review of Genomics and Human Genetics . 10 : 285-311
Journal article
see the publicationL’évolution des chromosomes sexuels humains
Biofutur . 304 : 40-41
Journal article
see the publication