Publications Evolution and Genomes

2024

Bastide, H., Legout, H., Dogbo, N., Ogereau, D., Prediger, C., Carcaud, J., Filée, J., Garnery, L., Gilbert, C., Marion-Poll, F., Requier, F., Sandoz, J.-C., Yassin, A., 2024. The genome of the blind bee louse fly reveals deep convergences with its social host and illuminates Drosophila origins. Current Biology 34, 1122-1132.e5. https://doi.org/10.1016/j.cub.2024.01.034

Da Lage, J.-L., Fontenelle, A., Filée, J., Merle, M., Béranger, J.-M., Almeida, C.E., Folly Ramos, E., Harry, M., 2024. Evidence that hematophagous triatomine bugs may eat plants in the wild. Insect Biochemistry and Molecular Biology 165, 104059. https://doi.org/10.1016/j.ibmb.2023.104059

Hearn, J., Gobbo, E., Nieves-Aldrey, J.L., Branca, A., Nicholls, J.A., Koutsovoulos, G., Lartillot, N., Stone, G.N., Ronquist, F., 2024. Phylogenomic analysis of protein-coding genes resolves complex gall wasp relationships. Systematic Entomology 49, 110–137. https://doi.org/10.1111/syen.12611

2023

Gilbert, C. and Maumus, F. (2023) ‘Sidestepping Darwin: horizontal gene transfer from plants to insects’, Current Opinion in Insect Science, 57, p. 101035. Available at: https://doi.org/10.1016/j.cois.2023.101035.

Petit, A.J.R., Guez, J. and Le Rouzic, A. (2023) ‘Correlated stabilizing selection shapes the topology of gene regulatory networks’, GENETICS. Edited by G. Martin, 224(2), p. iyad065. Available at: https://doi.org/10.1093/genetics/iyad065.

Tomar, S.S., Hua-Van, A. and Le Rouzic, A. (2023) ‘A population genetics theory for piRNA-regulated transposable elements’, Theoretical Population Biology, 150, pp. 1–13. Available at: https://doi.org/10.1016/j.tpb.2023.02.001.

Heisserer, C. et al. (2023) ‘Massive Somatic and Germline Chromosomal Integrations of Polydnaviruses in Lepidopterans’, Molecular Biology and Evolution, 40(3), p. msad050. Available at: https://doi.org/10.1093/molbev/msad050.

Filée, J. et al. (2023) ‘Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya’, Nature Communications, 14(1), p. 838. Available at: https://doi.org/10.1038/s41467-023-36487-z.

Da Lage, J.-L. et al. (2023) ‘Hematophagous triatomine bugs feed also on plants and express functional amylase’, bioRxiv, pp. 2023–03.

M. Rhimi et al. (2023) ‘Structural and functional characterization of Drosophila melanogaster α-amylase’, Molecules, 28, p. 5327. Available at: https://doi.org/10.3390/molecules28145327.

2022

Guilliet, J. et al. (2022) ‘What complete mitochondrial genomes tell us about the evolutionary history of the black soldier fly, Hermetia illucens’, BMC Ecology and Evolution, 22(1), p. 72. Available at: https://doi.org/10.1186/s12862-022-02025-6.

Muller, H. et al. (2022) ‘Investigating bracovirus chromosomal integration and inheritance in lepidopteran host and nontarget species’, Molecular Ecology, 31(21), pp. 5538–5551. Available at: https://doi.org/10.1111/mec.16685.

Hebra, T. et al. (2022) ‘Combining OSMAC, metabolomic and genomic methods for the production and annotation of halogenated azaphilones and ilicicolins in termite symbiotic fungi’, Scientific Reports, 12(1), p. 17310. Available at: https://doi.org/10.1038/s41598-022-22256-3.

Hayward, A. and Gilbert, C. (2022) ‘Transposable elements’, Current biology: CB, 32(17), pp. R904–R909. Available at: https://doi.org/10.1016/j.cub.2022.07.044.

de Vienne, D. and Capy, P. (2022) ‘Special issue on “The relationship between genotype and phenotype: new insight into an old question”’, Genetica, 150(3–4), p. 151. Available at: https://doi.org/10.1007/s10709-022-00153-x.

Chevin, L.-M. et al. (2022) ‘Using phenotypic plasticity to understand the structure and evolution of the genotype–phenotype map’, Genetica, 150(3–4), pp. 209–221. Available at: https://doi.org/10.1007/s10709-021-00135-5.

Pienaar, R.D. et al. (2022) ‘First Evidence of Past and Present Interactions between Viruses and the Black Soldier Fly, Hermetia illucens’, Viruses, 14(6), p. 1274. Available at: https://doi.org/10.3390/v14061274.

Merle, M. et al. (2022) ‘Genome Size Variation of Chagas Disease Vectors of the Rhodniini Tribe’, The American Journal of Tropical Medicine and Hygiene, 107(1), pp. 211–215. Available at: https://doi.org/10.4269/ajtmh.21-0394.

Le Rouzic, A. (2022) ‘Gene network robustness as a multivariate character’, Peer Community Journal, 2, p. e26. Available at: https://doi.org/10.24072/pcjournal.125.

Burban, E., Tenaillon, M.I. and Le Rouzic, A. (2022) ‘Gene network simulations provide testable predictions for the molecular domestication syndrome’, Genetics. Edited by A. Tellier, 220(2), p. iyab214. Available at: https://doi.org/10.1093/genetics/iyab214.

Gilbert, C. and Belliardo, C. (2022) ‘The diversity of endogenous viral elements in insects’, Current Opinion in Insect Science, 49, pp. 48–55. Available at: https://doi.org/10.1016/j.cois.2021.11.007.

Filee, J. et al. (2022) ‘Wolbachia genomics reveals a potential for a nutrition-based symbiosis in blood-sucking Triatomine bugs’, bioRxiv, pp. 2022–09.

2021

Capy, P. (2021) ‘Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes’, Cells, 10(12), p. 3590. Available at: https://doi.org/10.3390/cells10123590.

Scalvenzi, T. et al. (2021) ‘Gut microbial ecology of Xenopus tadpoles across life stages’, Peer Community Journal, 1, p. e41. Available at: https://doi.org/10.24072/pcjournal.53.

Muller, H., Loiseau, V., et al. (2021) ‘Assessing the Impact of a Viral Infection on the Expression of Transposable Elements in the Cabbage Looper Moth (Trichoplusia ni)’, Genome Biology and Evolution, 13(11), p. evab231. Available at: https://doi.org/10.1093/gbe/evab231.

Filée, J. et al. (2021) ‘Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution’, Mobile DNA, 12(1), p. 24. Available at: https://doi.org/10.1186/s13100-021-00252-0.

Muller, H., Chebbi, M.A., et al. (2021) ‘Genome-Wide Patterns of Bracovirus Chromosomal Integration into Multiple Host Tissues during Parasitism’, Journal of Virology. Edited by C.R. Parrish, 95(22), pp. e00684-21. Available at: https://doi.org/10.1128/JVI.00684-21.

Simion, P. et al. (2021) ‘Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga’, Science Advances, 7(41), p. eabg4216. Available at: https://doi.org/10.1126/sciadv.abg4216.

Desbiez-Piat, A. et al. (2021) ‘Interplay between extreme drift and selection intensities favors the fixation of beneficial mutations in selfing maize populations’, Genetics, 219(2). Available at: https://doi.org/10/gm5w52.

Feller, G., Bonneau, M. and Da Lage, J.-L. (2021) ‘Amyrel, a novel glucose-forming α-amylase from Drosophila with 4-α-glucanotransferase activity by disproportionation and hydrolysis of maltooligosaccharides’, Glycobiology, 31(9), pp. 1134–1144. Available at: https://doi.org/10.1093/glycob/cwab036.

Pélabon, C. et al. (2021) ‘Quantitative assessment of observed versus predicted responses to selection’, Evolution, 75(9), pp. 2217–2236. Available at: https://doi.org/10.1111/evo.14284.

Loiseau, V. et al. (2021) ‘Monitoring Insect Transposable Elements in Large Double-Stranded DNA Viruses Reveals Host-to-Virus and Virus-to-Virus Transposition’, Molecular Biology and Evolution, 38(9), pp. 3512–3530. Available at: https://doi.org/10.1093/molbev/msab198.

Gilbert, C. and Tengs, T. (2021) ‘No species-level losses of s2m suggests critical role in replication of SARS-related coronaviruses’, Scientific Reports, 11(1), p. 16145. Available at: https://doi.org/10.1038/s41598-021-95496-4.

Herpin, A. et al. (2021) ‘Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish’, Genome Research, 31(8), pp. 1366–1380. Available at: https://doi.org/10.1101/gr.274266.120.

Muller, H., Ogereau, D., et al. (2021) ‘Draft nuclear genome and complete mitogenome of the Mediterranean corn borer, Sesamia nonagrioides, a major pest of maize’, G3 (Bethesda, Md.), 11(7), p. jkab155. Available at: https://doi.org/10.1093/g3journal/jkab155.

Madi-Ravazzi, L. et al. (2021) ‘Integrative taxonomy and a new species description in the sturtevanti subgroup of the Drosophila saltans group (Diptera: Drosophilidae)’, Zootaxa, 4980(2), p. 269292. Available at: https://doi.org/10.11646/zootaxa.4980.2.3.

David, O., Le Rouzic, A. and Dillmann, C. (2021) ‘Optimization of sampling designs for pedigrees and association studies’, Biometrics [Preprint]. Available at: https://doi.org/10/gkbgs2.

Ducret, V. et al. (2021) ‘Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri’, BMC genomics, 22(1), p. 204. Available at: https://doi.org/10.1186/s12864-021-07517-1.

Devilliers, M. et al. (2021) ‘Differential metabolic sensitivity of insulin-like-response- and TORC1-dependent overgrowth in Drosophila fat cells’, Genetics. Edited by D. Andrew, 217(1), p. iyaa010. Available at: https://doi.org/10.1093/genetics/iyaa010.

Cormier, A. et al. (2021) ‘Comparative Genomics of Strictly Vertically Transmitted, Feminizing Microsporidia Endosymbionts of Amphipod Crustaceans’, Genome Biology and Evolution, 13(1), p. evaa245. Available at: https://doi.org/10.1093/gbe/evaa245.

Gilbert, C., Peccoud, J. and Cordaux, R. (2021) ‘Transposable Elements and the Evolution of Insects’, Annual Review of Entomology, 66, pp. 355–372. Available at: https://doi.org/10.1146/annurev-ento-070720-074650.

Gauthier, J. et al. (2021) ‘Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization’, Commun Biol, 4(1), p. 104. Available at: https://doi.org/10.1038/s42003-020-01623-8.

Wallace, M.A. et al. (2021) ‘The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe’, Virus Evolution, 7(1), p. veab031. Available at: https://doi.org/10.1093/ve/veab031.

Dhorne-Pollet, S., Pollet, N. and Barrey, E. (2021a) ‘A New Method for Sequencing the Mitochondrial Genome by Using Long Read Technology’, Methods in Molecular Biology (Clifton, N.J.), 2277, pp. 331–343. Available at: https://doi.org/10.1007/978-1-0716-1270-5_20.

Dhorne-Pollet, S., Pollet, N. and Barrey, E. (2021b) ‘A New Method for Sequencing the Mitochondrial Genome by Using Long Read Technology’, Methods in Molecular Biology (Clifton, N.J.), 2277, pp. 331–343. Available at: https://doi.org/10.1007/978-1-0716-1270-5_20.

G. Feller, M. Bonneau and Da Lage, J.-L. (2021) ‘Amyrel, a novel glucose-forming α-amylase from Drosophila with 4-α-glucanotransferase activity by disproportionation and hydrolysis of maltooligosaccharides’, Glycobiology, 31(9), pp. 1134–1144. Available at: https://doi.org/10.1093/glycob/cwab036.

2020

Dhorne-Pollet, S., Barrey, E. and 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, 21(1), p. 785. Available at: https://doi.org/10.1186/s12864-020-07183-9.

Renneville, C. et al. (2020) ‘Unidirectional response to bidirectional selection on body size. I. Phenotypic, life‐history, and endocrine responses’, Ecology and Evolution, 10(19), pp. 10571–10592. Available at: https://doi.org/10.1002/ece3.6713.

Le Rouzic, A. et al. (2020) ‘Unidirectional response to bidirectional selection on body size II. Quantitative genetics’, Ecology and Evolution, 10(20), pp. 11453–11466. Available at: https://doi.org/10.1002/ece3.6783.

Loiseau, V., Cordaux, R., et al. (2020) ‘Characterization of a new case of XMLV (Bxv1) contamination in the human cell line Hep2 (clone 2B)’, Scientific Reports, 10(1), p. 16046. Available at: https://doi.org/10.1038/s41598-020-73169-y.

Jallet, A.J., Le Rouzic, A. and Genissel, A. (2020) ‘Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant Pathogen Zymoseptoria tritici’, Frontiers in Microbiology, 11, p. 573829. Available at: https://doi.org/10.3389/fmicb.2020.573829.

Benoist, R. et al. (2020) ‘Quantitative Trait Loci involved in the reproductive success of a parasitoid wasp’, Molecular Ecology, p. mec.15567. Available at: https://doi.org/10/gg8nxz.

Rispe, C. et al. (2020) ‘The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest’, BMC biology, 18(1), p. 90. Available at: https://doi.org/10.1186/s12915-020-00820-5.

Becking, T., Gilbert, C. and Cordaux, R. (2020) ‘Impact of transposable elements on genome size variation between two closely related crustacean species’, Analytical Biochemistry, 600, p. 113770. Available at: https://doi.org/10.1016/j.ab.2020.113770.

Saint-Leandre, B. et al. (2020) ‘piRNA and Transposon Dynamics in Drosophila: A Female Story’, Genome Biology and Evolution. Edited by J. Gonzalez, 12(6), pp. 931–947. Available at: https://doi.org/10.1093/gbe/evaa094.

Scalvenzi, T., Clavereau, I. and Pollet, N. (2020) ‘Insights on the evolution of vertebrate microbiomes from the analysis of the Xenopus frog microbiota across life stages’, bioRxiv, p. 2020.05.25.110734. Available at: https://doi.org/10.1101/2020.05.25.110734.

Zhang, H.-H. et al. (2020) ‘Horizontal transfer and evolution of transposable elements in vertebrates’, Nature Communications, 11(1), p. 1362. Available at: https://doi.org/10.1038/s41467-020-15149-4.

Desiderato, A. et al. (2020) ‘Horizontal Transfer and Gene Loss Shaped the Evolution of Alpha-Amylases in Bilaterians’, G3 (Bethesda, Md.), 10(2), pp. 709–719. Available at: https://doi.org/10.1534/g3.119.400826.

Lima-Oliveira, T.M. et al. (2020) ‘Molecular eco-epidemiology on the sympatric Chagas disease vectors Triatoma brasiliensis and Triatoma petrocchiae: Ecotopes, genetic variation, natural infection prevalence by trypanosomatids and parasite genotyping’, Acta Tropica, 201, p. 105188. Available at: https://doi.org/10.1016/j.actatropica.2019.105188.

Loiseau, V., Herniou, E.A., et al. (2020) ‘Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses’, Virus Evolution, 6(1), p. vez060. Available at: https://doi.org/10.1093/ve/vez060.

Yubuki, N. et al. (2020) ‘Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina-Blastocystis Stramenopile Lineage’, Molecular Biology and Evolution, 37(3), pp. 651–659. Available at: https://doi.org/10.1093/molbev/msz250.

Zattera, M.L. et al. (2020) ‘Evolutionary Dynamics of the Repetitive DNA in the Karyotypes of Pipa carvalhoi and Xenopus tropicalis (Anura, Pipidae)’, Frontiers in Genetics, 11, p. 637. Available at: https://doi.org/10.3389/fgene.2020.00637.

2019

Courret, C. et al. (2019) ‘Meiotic drive mechanisms: lessons from Drosophila’, Proceedings of the Royal Society B: Biological Sciences, 286(1913), p. 20191430. Available at: https://doi.org/10.1098/rspb.2019.1430.

Becking, T. et al. (2019) ‘Sex chromosomes control vertical transmission of feminizing Wolbachia symbionts in an isopod’, PLoS biology, 17(10), p. e3000438. Available at: https://doi.org/10.1371/journal.pbio.3000438.

Attardo, G.M. et al. (2019) ‘Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes’, Genome Biol, 20(1), p. 187. Available at: https://doi.org/10.1186/s13059-019-1768-2.

Hardwick, K.M. et al. (2019) ‘Draft Genome of Busseola fusca, the Maize Stalk Borer, a Major Crop Pest in Sub-Saharan Africa’, Genome Biology and Evolution, 11(8), pp. 2203–2207. Available at: https://doi.org/10.1093/gbe/evz166.

Machado, L.C. et al. (2019) ‘Genome sequencing reveals coinfection by multiple chikungunya virus genotypes in a recent outbreak in Brazil’, PLoS neglected tropical diseases, 13(5), p. e0007332. Available at: https://doi.org/10.1371/journal.pntd.0007332.

Chebbi, M.A. et al. (2019) ‘The Genome of Armadillidium vulgare (Crustacea, Isopoda) Provides Insights into Sex Chromosome Evolution in the Context of Cytoplasmic Sex Determination’, Molecular Biology and Evolution, 36(4), pp. 727–741. Available at: https://doi.org/10.1093/molbev/msz010.

Reiss, D. et al. (2019) ‘Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot’, PLoS genetics, 15(2), p. e1007965. Available at: https://doi.org/10.1371/journal.pgen.1007965.

Da Lage, J.-L. et al. (2019) ‘Evolution of salivary glue genes in Drosophila species’, BMC evolutionary biology, 19(1), p. 36. Available at: https://doi.org/10.1186/s12862-019-1364-9.

Schneider, D.I. et al. (2019) ‘Symbiont-Driven Male Mating Success in the Neotropical Drosophila paulistorum Superspecies’, Behavior Genetics, 49(1), pp. 83–98. Available at: https://doi.org/10.1007/s10519-018-9937-8.

2018

Filée, J. (2018) ‘Giant viruses and their mobile genetic elements: the molecular symbiosis hypothesis’, Current Opinion in Virology, 33, pp. 81–88. Available at: https://doi.org/10.1016/j.coviro.2018.07.013.

Pereira, C.M. et al. (2018) ‘The somatic mobilization of transposable element mariner-Mos1 during the Drosophila lifespan and its biological consequences’, Gene, 679, pp. 65–72. Available at: https://doi.org/10.1016/j.gene.2018.08.079.

Thomas-Bulle, C. et al. (2018) ‘Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics’, BMC genomics, 19(1), p. 821. Available at: https://doi.org/10.1186/s12864-018-5200-1.

Bichang’a, G. et al. (2018) ‘α-Amylase Mediates Host Acceptance in the Braconid Parasitoid Cotesia flavipes’, Journal of Chemical Ecology, 44(11), pp. 1030–1039. Available at: https://doi.org/10.1007/s10886-018-1002-9.

Odorico, A., Rünneburger, E. and Le Rouzic, A. (2018) ‘Modelling the influence of parental effects on gene‐network evolution’, Journal of Evolutionary Biology, 31(5), pp. 687–700. Available at: https://doi.org/10.1111/jeb.13255.

Becking, T. et al. (2018) ‘Author Correction: Diversity and evolution of sex determination systems in terrestrial isopods’, Scientific Reports, 8(1), p. 6948. Available at: https://doi.org/10.1038/s41598-018-25423-7.

Gaulin, E. et al. (2018) ‘Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation’, BMC biology, 16(1), p. 43. Available at: https://doi.org/10.1186/s12915-018-0508-5.

Guyeux, C. et al. (2018) ‘Theoretical Study of the One Self-Regulating Gene in the Modified Wagner Model’, Mathematics, 6(4), p. 58. Available at: https://doi.org/10.3390/math6040058.

Gilbert, C. and Feschotte, C. (2018) ‘Horizontal acquisition of transposable elements and viral sequences: patterns and consequences’, Current Opinion in Genetics & Development, 49, pp. 15–24. Available at: https://doi.org/10.1016/j.gde.2018.02.007.

Peccoud, J. et al. (2018) ‘A Survey of Virus Recombination Uncovers Canonical Features of Artificial Chimeras Generated During Deep Sequencing Library Preparation’, G3 (Bethesda, Md.), 8(4), pp. 1129–1138. Available at: https://doi.org/10.1534/g3.117.300468.

Peccoud, J., Cordaux, R. and Gilbert, C. (2018) ‘Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects’, BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology, 40(2). Available at: https://doi.org/10.1002/bies.201700177.

Lewis, S.H. et al. (2018) ‘Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements’, Nature Ecology & Evolution, 2(1), pp. 174–181. Available at: https://doi.org/10.1038/s41559-017-0403-4.

Bichang’a, G.B. et al. (2018) ‘Salivary a-Amylase of Stem Borer Hosts Determines Host Recognition and Acceptance for Oviposition by Cotesia spp. (Hymenoptera, Braconidae)’, Frontiers in Ecology and Evolution, 6, p. doi: 10.3389/fevo.2018.00228.

Da Lage, J.-L. (2018) ‘The Amylases of Insects’, International Journal of Insect Science, 10, p. 1179543318804783. Available at: https://doi.org/10.1177/1179543318804783.