Evolution and genomes

 03/07/2021 -  EGCE
The team “Evolution and genomes” is interested in the evolution of the structure and function of genomes, at the organisms or populations or species scale.

Co leaders :
Nicolas Pollet (CNRS) Aurélie Hua-Van (UPSay)

Topics

Dynamics and evolution of the genomes: Impact of selfish genes (Transposable elements, meiotic distorter) and polyploidization. Interactions within genomes, especially at the scale of gene networks which are part of phenotype realisation or help developmental or physiological or of the cellular cycle processes to be set up. Genetic and epigenetic factors in evolution and adaptation.

Approaches

Compared biology, Genomics, Population genetics, Theoretical biology. All use the tools of molecular biology and of bio-informatics, and lead to the making of scripts and specific tools for research/sequence analysis (molecular evolution, phylogeny) and for high throuput data treatment.

Members

Publications

  • Bacela-Spychalska K., Wattier R., Teixeira M., Cordaux R. , Quiles A., Grabowski M., Wroblewski P., Ovcharenko M., Grabner D., Weber D., Weigand AM., Rigaud T., Dillman AR.. (2023) Widespread infection, diversification and old host associations of Nosema Microsporidia in European freshwater gammarids (Amphipoda). PLoS Pathog, 8 (19) e1011560
  • Filée J. , Becker HF., Mellottee L., Eddine RZ., Li Z., Yin W., Lambry JC., Liebl U., Myllykallio H.. (2023) Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya. Nat Commun, 1 (14) 838
  • Gilbert C. , Maumus F.. (2023) Sidestepping Darwin: horizontal gene transfer from plants to insects. Current Opinion in Insect Science, (57) 101035
  • Heisserer C., Muller H., Jouan V., Musset K., Periquet G., Drezen JM., Volkoff AN., Gilbert C. , O’Connell M.. (2023) Massive Somatic and Germline Chromosomal Integrations of Polydnaviruses in Lepidopterans. Molecular Biology and Evolution, 3 (40) msad050
  • Petit AJR., Guez J., Le Rouzic A. , Martin G.. (2023) Correlated stabilizing selection shapes the topology of gene regulatory networks. GENETICS, 2 (224) iyad065
  • Tomar SS., Hua-Van A. , Le Rouzic A. . (2023) A population genetics theory for piRNA-regulated transposable elements. Theoretical Population Biology, (150) 1-13
  • Burban E., Tenaillon MI., Le Rouzic A. . (2022) Gene network simulations provide testable predictions for the molecular domestication syndrome. Genetics, 2 (220) iyab214
  • Chevin LM., Leung C., Le Rouzic A. , Uller T.. (2022) Using phenotypic plasticity to understand the structure and evolution of the genotype–phenotype map. Genetica, 3-4 (150) 209-221
  • Guilliet J., Baudouin G., Pollet N. , Filée J. . (2022) What complete mitochondrial genomes tell us about the evolutionary history of the black soldier fly, Hermetia illucens. BMC Ecol Evol, 1 (22) 72
  • Hebra T., Pollet N. , Touboul D., Eparvier V.. (2022) Combining OSMAC, metabolomic and genomic methods for the production and annotation of halogenated azaphilones and ilicicolins in termite symbiotic fungi. Sci Rep, 1 (12) 17310
  • Le Rouzic A. . (2022) Gene network robustness as a multivariate character. Peer Community Journal, (2) e26
  • David O., Le Rouzic A. , Dillmann C.. (2021) Optimization of sampling designs for pedigrees and association studies. Biometrics,
  • Desbiez-Piat A., Le Rouzic A. , Tenaillon MI., Dillmann C.. (2021) Interplay between extreme drift and selection intensities favors the fixation of beneficial mutations in selfing maize populations. Genetics, 2 (219)
  • Devilliers M., Garrido D., Poidevin M., Rubin T., Le Rouzic A. , Montagne J., Andrew D.. (2021) Differential metabolic sensitivity of insulin-like-response- and TORC1-dependent overgrowth in Drosophila fat cells. Genetics, 1 (217) iyaa010
  • Gauthier J., Boulain H., van Vugt JJFA., Baudry L., Persyn E., Aury JM., Noel B., Bretaudeau A., Legeai F., Warris S., Chebbi MA., Dubreuil G., Duvic B., Kremer N., Gayral P., Musset K., Josse T., Bigot D., Bressac C., Moreau S., Periquet G., Harry M., Montagné N., Boulogne I., Sabeti-Azad M., Maïbèche M., Chertemps T., Hilliou F., Siaussat D., Amselem J., Luyten I., Capdevielle-Dulac C., Labadie K., Merlin BL., Barbe V., de Boer JG., Marbouty M., Cônsoli FL., Dupas S., Hua-Van A. , Le Goff G., Bézier A., Jacquin-Joly E., Whitfield JB., Vet LEM., Smid HM., Kaiser L., Koszul R., Huguet E., Herniou EA., Drezen JM.. (2021) Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol, 1 (4) 104
  • Herpin A., Schartl M., Depincé A., Guiguen Y., Bobe J., Hua-Van A. , Hayman ES., Octavera A., Yoshizaki G., Nichols KM., Goetz GW., Luckenbach JA.. (2021) Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish. Genome Res., 8 (31) 1366-1380
  • Pélabon C., Albertsen E., Rouzic AL., Firmat C., Bolstad GH., Armbruster WS., Hansen TF.. (2021) Quantitative assessment of observed versus predicted responses to selection. Evolution, 9 (75) 2217-2236
  • Scalvenzi T., Clavereau I. , Bourge M., Pollet N. . (2021) Gut microbial ecology of Xenopus tadpoles across life stages. Peer Community Journal, e41 (1) 2020.05.25.110734
  • Benoist R., Capdevielle‐Dulac C., Chantre C., Jeannette R., Calatayud PA., Drezen JM., Dupas S., Le Rouzic A. , Le Ru B., Moreau L., Van Dijk E., Kaiser L., Mougel F.. (2020) Quantitative Trait Loci involved in the reproductive success of a parasitoid wasp. Mol Ecol, mec.15567
  • Dhorne-Pollet S., Barrey E., Pollet N. . (2020) A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants. BMC Genomics, 1 (21) 785
  • Jallet AJ., Le Rouzic A. , Genissel A.. (2020) Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant Pathogen Zymoseptoria tritici. Front. Microbiol., (11) 573829
  • Le Rouzic A. , Renneville C., Millot A., Agostini S., Carmignac D., Édeline Éric.. (2020) Unidirectional response to bidirectional selection on body size II. Quantitative genetics. Ecology and Evolution, 20 (10) 11453-11466
  • Renneville C., Millot A., Agostini S., Carmignac D., Maugars G., Dufour S., Le Rouzic A. , Edeline E.. (2020) Unidirectional response to bidirectional selection on body size. I. Phenotypic, life‐history, and endocrine responses. Ecol Evol, 19 (10) 10571-10592
  • Saint-Leandre B., Capy P., Hua-Van A. , Filée J. , Gonzalez J.. (2020) piRNA and Transposon Dynamics in Drosophila: A Female Story. Genome Biology and Evolution, 6 (12) 931-947
  • Scalvenzi T., Clavereau I. , Pollet N. . (2020) Insights on the evolution of vertebrate microbiomes from the analysis of the Xenopus frog microbiota across life stages. bioRxiv, 2020.05.25.110734
  • Yubuki N., Galindo LJ., Reboul G., López-García P., Brown MW., Pollet N. , Moreira D.. (2020) Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina-Blastocystis Stramenopile Lineage. Mol Biol Evol, 3 (37) 651-659
  • Zattera ML., Gazolla CB., Soares AA., Gazoni T., Pollet N. , Recco-Pimentel SM., Bruschi DP.. (2020) Evolutionary Dynamics of the Repetitive DNA in the Karyotypes of Pipa carvalhoi and Xenopus tropicalis (Anura, Pipidae). Front Genet, (11) 637
  • Attardo GM., Abd-Alla AMM., Acosta-Serrano A., Allen JE., Bateta R., Benoit JB., Bourtzis K., Caers J., Caljon G., Christensen MB., Farrow DW., Friedrich M., Hua-Van A. , Jennings EC., Larkin DM., Lawson D., Lehane MJ., Lenis VP., Lowy-Gallego E., Macharia RW., Malacrida AR., Marco HG., Masiga D., Maslen GL., Matetovici I., Meisel RP., Meki I., Michalkova V., Miller WJ., Minx P., Mireji PO., Ometto L., Parker AG., Rio R., Rose C., Rosendale AJ., Rota-Stabelli O., Savini G., Schoofs L., Scolari F., Swain MT., Takáč P., Tomlinson C., Tsiamis G., Van Den Abbeele J., Vigneron A., Wang J., Warren WC., Waterhouse RM., Weirauch MT., Weiss BL., Wilson RK., Zhao X., Aksoy S.. (2019) Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biol, 1 (20) 187
  • Debat V., Le Rouzic A. . (2019) Canalization, a central concept in biology. Seminars in Cell & Developmental Biology, (88) 1-3
  • Schneider DI., Ehrman L., Engl T., Kaltenpoth M., Hua-Van A. , Le Rouzic A. , Miller WJ.. (2019) Symbiont-Driven Male Mating Success in the Neotropical Drosophila paulistorum Superspecies. Behav Genet, 1 (49) 83-98
  • Guyeux C., Couchot JF., Le Rouzic A. , Bahi J., Marangio L.. (2018) Theoretical Study of the One Self-Regulating Gene in the Modified Wagner Model. Mathematics, 4 (6) 58
  • Odorico A., Rünneburger E., Le Rouzic A. . (2018) Modelling the influence of parental effects on gene‐network evolution. J. Evol. Biol., 5 (31) 687-700
  • Bouallègue M., Rouault JD., Hua-Van A. , Makni M., Capy P.. (2017) Molecular Evolution of piggyBac Superfamily: From Selfishness to Domestication. Genome Biol Evol, 2 (9) 323-339
  • Bronchain OJ., Chesneau A., Monsoro-Burq AH., Jolivet P., Paillard E., Scanlan TS., Demeneix BA., Sachs LM., Pollet N. . (2017) Implication of thyroid hormone signaling in neural crest cells migration: Evidence from thyroid hormone receptor beta knockdown and NH3 antagonist studies. Mol Cell Endocrinol, (439) 233-246
  • Denis B., Claisse G., Le Rouzic A. , Wicker-Thomas C., Lepennetier G., Joly D.. (2017) Male accessory gland proteins affect differentially female sexual receptivity and remating in closely related Drosophila species. Journal of Insect Physiology, (99) 67-77
  • Maharana SK., Pollet N. , Schlosser G.. (2017) Identification of novel cis-regulatory elements of Eya1 in Xenopus laevis using BAC recombineering. Sci Rep, 1 (7) 15033
  • Saint-Leandre B., Clavereau I. , Hua-Van A. , Capy P.. (2017) Transcriptional polymorphism of pi RNA regulatory genes underlies the mariner activity in Drosophila simulans testes. Mol Ecol, 14 (26) 3715-3731
  • Spirhanzlova P., Dhorne-Pollet S., Fellah JS., Da Silva C., Tlapakova T., Labadie K., Weissenbach J., Poulain J., Jaffredo T., Wincker P., Krylov V., Pollet N. . (2017) Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis. Dev Biol, 2 (426) 255-260
  • Helleu Q., Gérard P., Dubruille R., Ogereau D. , Prud'homme B., Loppin B., Montchamp-Moreau C. . (2016) Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive. Proceedings of the National Academy of Sciences of the United States of America, 15 (113) 4110 - 4115
  • Le Rouzic A. , Álvarez-Castro JM.. (2016) Epistasis-Induced Evolutionary Plateaus in Selection Responses. The American Naturalist, 6 (188) E134-E150
  • Renneville C., Rouzic AL., Baylac M., Millot A., Loisel S., Edeline E.. (2016) Morphological drivers of trophic cascades. Oikos, 8 (125) 1193-1202
  • Robillard E. , Le Rouzic A. , Zhang Z., Capy P., Hua-Van A. . (2016) Experimental evolution reveals hyperparasitic interactions among transposable elements. Proc. Natl. Acad. Sci. U.S.A., 51 (113) 14763-14768
  • Rünneburger E., Le Rouzic A. . (2016) Why and how genetic canalization evolves in gene regulatory networks. BMC Evol Biol, 1 (16) 239
  • Wallau GL., Capy P., Loreto E., Le Rouzic A. , Hua-Van A. . (2016) VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila. Mol Biol Evol, 4 (33) 1094-1109
  • Bougerol M., Auradé F., Lambert FM., Le Ray D., Combes D., Thoby-Brisson M., Relaix F., Pollet N. , Tostivint H.. (2015) Generation of BAC Transgenic Tadpoles Enabling Live Imaging of Motoneurons by Using the Urotensin II-Related Peptide (ust2b) Gene as a Driver. PLoS ONE, 2 (10) e0117370
  • Colombo BM., Scalvenzi T., Benlamara S., Pollet N. . (2015) Microbiota and mucosal immunity in amphibians. Front Immunol, (6) 111
  • Filée J. , Rouault JD., Harry M., Hua-Van A. . (2015) Mariner transposons are sailing in the genome of the blood-sucking bug Rhodnius prolixus. BMC Genomics, (16) 1061
  • Gasmi L., Boulain H., Gauthier J., Hua-Van A. , Musset K., Jakubowska AK., Aury JM., Volkoff AN., Huguet E., Herrero S., Drezen JM.. (2015) Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses. PLoS Genet, 9 (11) e1005470
  • Hoen DR., Hickey G., Bourque G., Casacuberta J., Cordaux R. , Feschotte C., Fiston-Lavier AS., Hua-Van A. , Hubley R., Kapusta A., Lerat E., Maumus F., Pollock DD., Quesneville H., Smit A., Wheeler TJ., Bureau TE., Blanchette M.. (2015) A call for benchmarking transposable element annotation methods. Mobile DNA, 1 (6) 13
  Equipe
  Symbiotic and holobiotic interactions Processes of genome evolution Selfish genetic elements Gene network modelling Molecular evolution Genotype-phenotype interactions