Clément Gilbert

CNRS researcher (CRCN, HDR)

Laboratoire Evolution, Génomes, Comportement, Ecologie
CNRS Université Paris-Saclay UMR 9191 IRD UMR 247
12 route 128, 91190 Gif sur Yvette
France
email: clement.gilbert1@universite-paris-saclay.fr
Tel: +33 1 69 15 49 85

RESEARCH

Evolution of resistance to natural gene drive systems

Funding: ANR PRC (RESIST), March 2022 – Feb. 2026. Position: Leader of a work package in collaboration with Catherine Montchamp-Moreau and Cécile Courret. PI: R. Cordaux (UMR EBI, Université de Poitiers)

Role of sympatry in shaping horizontal transfer of transposable elements in insects

Funding: ANR PRC (TranspHorizon), Jan. 2019 – June 2024. Position: Leader of a work package. PI: A. Hua-Van (UMR CNRS EGCE 9191, Université Paris-Saclay)

Genomic interactions between parasitoid wasps and their lepidopteran hosts

Funding: ANR PRC (CoteBio), Apr. 2018 – Dec. 2023. Position: Co-leader with Prof. Elisabeth Huguet of a work package. PI: L. Kaiser (UMR CNRS EGCE 9191, Université Paris-Saclay)

Role of viruses as vectors of horizontal transfer of genetic material between animals

Funding: ANR JCJC (15-CE32-0011-01 TransVir), Nov. 2015 – Nov. 2021. PI: C. Gilbert

Impact of feminizing symbionts on the evolution of sex determination systems

Funding: ANR PRC (15-CE32-0006-01), Jan. 2016 – Jan. 2021. Position: Collaborator. PI: R. Cordaux (UMR CNRS EBI 7267, Université de Poitiers)

PUBLICATIONS

#equal contribution

Google Scholar: https://scholar.google.fr/citations?hl=fr&user=U5WMppQAAAAJ&view_op=list_works&pagesize=100

in press

Muller H, Heisserer C, Fortuna T, Mougel F, Huguet E, Kaiser L, Gilbert C. Investigating bracovirus chromosomal integration and inheritance in lepidopteran host and nontarget species. Mol Ecol.
Gilbert C^#, Maumus F.^# Multiple horizontal acquisitions of plant genes in the whitefly Bemisia tabaci.
Genome Biol Evol.

2022

Hayward A, Gilbert C. Transposable elements. Curr Biol. 32(17): R904-R909.
Pienaar RD, Gilbert C, Belliardo C, Herrero S, Herniou EA. First Evidence of Past and Present Interactions between Viruses and the Black Soldier Fly, Hermetia illucens. Viruses. 14(6):1274.
Gilbert C, Belliardo C. The diversity of endogenous viral elements in insects. Curr Opin Insect Sci. 49:48-55.

2021

Muller H, Loiseau V, Guillier S, Cordaux R, Gilbert C. Assessing the Impact of a Viral Infection on the Expression of Transposable Elements in the Cabbage Looper Moth (Trichoplusia ni). Genome Biol Evol. 13(11): evab231.
Muller H, Chebbi MA, Bouzar C, Périquet G, Fortuna T, Calatayud PA, Le Ru B, Obonyo J, Kaiser L, Drezen JM, Huguet E, Gilbert C. Genome-Wide Patterns of Bracovirus Chromosomal Integration into Multiple Host Tissues during Parasitism. J Virol. 95(22): e0068421.
Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot JF, Van Doninck K. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Sci Adv. 7(41): eabg4216.
Loiseau V, Peccoud J, Bouzar C, Guillier S, Fan J, Gueli Alletti G, Meignin C, Herniou EA, Federici BA, Wennmann JT, Jehle JA, Cordaux R, Gilbert C. Monitoring Insect Transposable Elements in Large Double-Stranded DNA Viruses Reveals Host-to-Virus and Virus-to-Virus Transposition. Mol Biol Evol. 38(9):3512-3530.
Gilbert C, Tengs T. No species-level losses of s2m suggests critical role in replication of SARS-related coronaviruses. Scientific reports: 11(1):16145.
Muller H, Ogereau D, Da-Lage JL, Capdevielle C, Pollet N, Fortuna T, Jeannette R, Kaiser L, Gilbert C. Draft nuclear genome and complete mitogenome of the Mediterranean corn borer, Sesamia nonagrioides, a major pest of maize. G3 (Bethesda). 11(7): jkab155.
Wallace MA, Coffman KA, Gilbert C, Ravindran S, Albery GF, Abbott J, Argyridou E, Bellosta P, Betancourt AJ, Colinet H, Eric K, Glaser-Schmitt A, Grath S, Jelic M, Kankare M, Kozeretska I, Loeschcke V, Montchamp-Moreau C, Ometto L, Onder BS, Orengo DJ, Parsch J, Pascual M, Patenkovic A, Puerma E, Ritchie MG, Rota-Stabelli O, Schou MF, Serga SV, Stamenkovic-Radak M, Tanaskovic M, Veselinovic MS, Vieira J, Vieira CP, Kapun M, Flatt T, González J, Staubach F, Obbard DJ. The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe. Virus Evol. 7(1): veab031.
Cormier A., Chebbi M.A., Giraud I., Wattier R., Teixeira M., Gilbert C., Rigaud T., Cordaux R. Comparative genomics of strictly vertically transmitted, feminizing microsporidia endosymbionts of amphipod crustaceans. Genome Biol. Evol. 13(1):evaa245.
Gilbert C., Peccoud J., Cordaux R. Transposable Elements and the Evolution of Insects. Annual Review of Entomology. 66.

2020

Loiseau V., Cordaux R., Giraud I., Beby-Defaux A., Lévêque N., Gilbert C. Characterization of a new case of XMLV (Bxv1) contamination in the human cell line Hep2 (clone 2B). Scientific reports: 10 (1), 1-8.
Becking T., Gilbert C., Cordaux R. Impact of transposable elements on genome size variation between two closely related crustacean species. Analytical Biochemistry, 113770.
Zhang H.H., Peccoud J., Zhang X.G., Gilbert C. Horizontal transfer and evolution of transposable elements in vertebrates. Nature Communications 11 (1), 1-10.
Desiderato A, Barbeitos M, Gilbert C, Da Lage JL. Horizontal Transfer and Gene Loss Shaped the Evolution of Alpha-Amylases in Bilaterians. G3 (Bethesda). 2020 Feb 6;10(2):709-719. doi: 10.1534/g3.119.400826.
Loiseau V, Herniou EA, Moreau Y, Lévêque N, Meignin C, Daeffler L, Federici B, Cordaux R, Gilbert C. Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses. Virus Evol. 2020 Jan 27;6(1):vez060. doi: 10.1093/ve/vez060.

2019

Becking T, Chebbi MA, Giraud I, Moumen B, Laverré T, Caubet Y, Peccoud J, Gilbert C#, Cordaux R#. Sex chromosomes control vertical transmission of feminizing Wolbachia symbionts in an isopod. PLoS Biol. 17(10):e3000438.
Machado LC, de Morais-Sobral MC, Campos TL, Pereira MR, de Albuquerque MFPM, Gilbert C, Franca RFO, Wallau GL. Genome sequencing reveals coinfection by multiple chikungunya virus genotypes in a recent outbreak in Brazil. PLoS Negl Trop Dis. 2019 13(5):e0007332.
Chebbi MA, Becking T, Moumen B, Giraud I, Gilbert C, Peccoud J, Cordaux R. The Genome of Armadillidium vulgare (Crustacea, Isopoda) Provides Insights into Sex Chromosome Evolution in the Context of Cytoplasmic Sex Determination. Mol Biol Evol. 36(4):727-741.
Reiss D, Mialdea G, Miele V, de Vienne DM, Peccoud J, Gilbert C, Duret L, Charlat S. Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot. PLoS Genet. 15(2):e1007965.
Grandjean F#, Gilbert C#, Razafimafondy F, Vucić M, Delaunay C, Gindre P, Bouchard J, Raimond M, Moumen B. A new bunya-like virus associated with mass mortality of white-clawed crayfish in the wild. Virology. 533:115-124.

2018

Gaulin, E., M. J. C. Pel, L. Camborde, H. San-Clemente, S. Courbier, M.-A. Dupouy, J. Lengelle, M. Veyssiere, A. Le Ru, F. Grandjean, R. Cordaux, B. Moumen, C. Gilbert, L. M. Cano, J.-M. Aury, J. Guy, P. Wincker, O. Bouchez, C. Klopp & B. Dumas (2018) Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation. BMC Biology, 16. 10.1186/s12915-018-0508-5.
Gilbert, C. & C. Feschotte (2018) Horizontal acquisition of transposable elements and viral sequences: patterns and consequences. Current opinion in genetics & development, 49, 15-24.
Lewis, S., K. Quarles, Y. Yang, M. Tanguy, L. Frezal, S. Smith, P. Sharma, R. Cordaux, C. Gilbert, I. Giraud, D. Collins, P. Zamore, E. Miska, P. Sarkies & F. Jiggins (2018) Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements. Nature Ecology & Evolution,10.1038/s41559-017-0403-4.
Peccoud, J., R. Cordaux & C. Gilbert (2018a) Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects. BioEssays 40(2).
Peccoud, J., S. Lequime, I. Moltini-Conclois, I. Giraud, L. Lambrechts & C. Gilbert (2018b) A Survey of Virus Recombination Uncovers Canonical Features of Artificial Chimeras Generated During Deep Sequencing Library Preparation. G3 (Bethesda), 8, 1129-1138.

2017

Cordaux R., Gilbert C. Evolutionary significance of Wolbachia-to-animal horizontal gene transfer: female sex determination and the f element in the isopod Armadillidium vulgare. Genes 8(7): 186.
Peccoud J., Chebbi M.A., Cormier A., Moumen B., Gilbert C., Marcadé I., Chandler C., Cordaux R. Untangling heteroplasmy, structure, and evolution of an atypical mitochondrial genome by PacBio sequencing. Genetics 207: 269-280.
Gilbert C., Cordaux R. Viruses as vectors of horizontal transfer of transposable elements. Curr. Opin. Virol. 25: 16-22.
Loiseau V., Giraud I., Federici B., Bigot Y., Cordaux R., Gilbert C. Iridovirus IIV31: a remarkable virus infecting terrestrial isopods. Virologie 21 : 147-149.
Peccoud J., Loiseau V., Cordaux R., Gilbert C. Massive horizontal transfer of transposable elements in insects. Proc. Natl. Acad. Sci. USA 114(18): 4721-4726.
Becking T.*, Giraud I., Raimond M., Moumen B., Chandler C., Cordaux R.^#, Gilbert C.^# Diversity and evolution of sex determination systems in terrestrials isopods. Sci. Rep. 7: 1084.

2016

Leclercq S., Thézé J., Chebbi MA, Giraud I, Moumen B, Ernenwein L., Grève P., Gilbert C., Cordaux R. Birth of a W sex chromosome by horizontal transfer of Wolbachia bacterial symbiont genome. Proc. Natl. Acad. Sci. USA 113(52): 15036–15041.
Gilbert C., Feschotte C. Virus et gènes viraux endogènes : évolution et impact. Virologie 20(3) : 158 – 173.
Gilbert C., Peccoud J., Chateigner A., Moumen B., Cordaux R^#., Herniou E^#. Continuous influx of genetic material from host to virus populations. PLOS Genet. 12 (2), e1005838

2015

Metegnier G., Becking T., Chebbi M.A., Giraud I., Moumen B., Schaack S., Cordaux R., Gilbert C. Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups. Mob. DNA 6: 16.
Cerveau N., Gilbert C., Liu C., Garrett R.A., Grève P., Bouchon D., Cordaux R. Genomic context drives transcription of insertion sequences in the bacterial endosymbiont Wolbachia wVulC. Gene 564: 81-86.

2014

Thézé J., Leclercq S., Moumen B., Cordaux R., Gilbert C. Remarkable diversity of endogenous viruses in a crustacean isopod. Genome Biol. Evol. 6(8): 2129–2140.
Gilbert C., Meik J.M., Card D.C., Castoe T.A., Schaack S. Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes. Proc. Biol. Soc. B 281: 1791.
Dupeyron M.*, Leclercq S., Cerveau N., Bouchon D., Gilbert C. Horizontal transfer of transposons within and between insects and crustaceans. Mob. DNA 5:4.
Gilbert C., Chateigner A., Ernenwein L., Bézier A., Barbe V., Herniou E.^#, Cordaux R.^# Population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons. Nature Commun. 5: 3348.

2013

Gilbert C., Cordaux R. Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes. Genome Biol Evol. 5: 822 – 832.
Gilbert C., Waters P.D., Feschotte C., Schaack S. Horizontal transfer of OC1 transposons in the Tasmanian devil. BMC Genomics 14: 134.

2012

Leclercq S., Gilbert C., Cordaux R. Cargo capacity of phages and plasmids and other factors influencing horizontal transfers of prokaryote transposable elements. Mobile Genetic Elements 2: 115-118.
Feschotte C., Gilbert C. Endogenous viruses: insights into viral evolution and impact on host biology. Nature Rev. Genetics 13: 283-296.
Al Nadaf S., Deakin J.E., Gilbert C., Robinson T.J., Graves J.A., Waters P.D. A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation. Chromosoma 121: 71-78.
Gilbert C., Hernandez S., Flores-Benabib J., Smith E., Feschotte C. Rampant horizontal transfer of SPIN transposons in squamate reptiles. Mol. Biol. Evol. 29: 503-515.

2011

Solano E., Gilbert C., Richards L., Taylor P. J., Soarimalala V., Engelbrecht A., Goodman S.M., Robinson T. J. First karyotypic descriptions of Malagasy rodents (Nesomyinae, Muridae) reveal variation at multiple taxonomic levels. J. Zool. 285: 110-118.
Chaumeil J., Waters P. D., Koina E., Gilbert C., Robinson T. J., Marshall Graves J. A. Evolution of XIST-controlled X chromosome inactivation: Epigenetic modifications in distantly related mammals. PLoS ONE 6: e19040.

2010

Gilbert C., Feschotte C. Genomic fossils calibrate the long-term evolution of hepatitis B viruses. PLoS Biol. 8: 9: e1000495.
Schaack S. R.^#, Gilbert C.^#, Feschotte C. Promiscous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol. Evol. 25: 537-546.
Gilbert C.^#, Schaack S. R.^#, Pace II J. K., Brindley P. J., Feschotte C. A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature 464: 1347 – 1350.

2009

Rodríguez Delgado C.L., Waters P.D., Gilbert C., Robinson T.J., Marshall Graves J.A. Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years. Chromosome Res. 17: 833 – 945.
Gilbert C., Maxfield D. G.*, Goodman S. M., Feschotte C. Parallel germline infiltration of a lentivirus in two Malagasy lemurs. PLOS Genet. 5: 3: e1000425.
Gilbert C., Pace II J. K., Feschotte C. Horizontal SPINning of transposons. Commun. Integr. Biol. 2: 117 – 119.

2008

Ropiquet A., Gerbault-Seureau M., Deuve J. L., Gilbert C., Pagacova E., Chai N., Rubes J., Hassanin A., Chromosome evolution in the subtribe Bovina (Mammalia, Bovidae): The karyotype of the Cambodian banteng (Bos javanicus birmanicus) suggests that Robertsonian translocations are related to interspecific hybridization. Chromosome Res. 16: 1107 – 1118.
Pace II J. K., Gilbert C., Clark M.*, Feschotte C. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc. Natl. Acad. Sci. USA 105: 17023 – 17028.
Gilbert C., Pace II J. K., Waters P. D. Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome. Gene 425: 1 – 8.
Gilbert C., Maree S., Robinson T. J. Chromosomal evolution and distribution of telomeric repeats in golden moles. Cytogenet. Genome Res. 121: 110 – 119.

2007

Gilbert C., Goodman S.M., Soarimalala V., Olson L.E., O’Brien P.C.M., Elder F.F.B., Yang F., Ferguson-Smith M.A., and Robinson T.J. Chromosomal evolution in tenrecs (Microgale and Oryzorictes, Tenrecidae) from the Central Highlands of Madagascar. Chromosome Res. 15: 1075 – 1091.

2006

Gilbert C., O’Brien P.C., Bronner G., Yang F., Hassanin A., Ferguson-Smith M.A., Robinson T. J. Chromosome painting and molecular dating indicate a low rate of chromosomal evolution in golden moles (Mammalia, Chrysochloridae). Chromosome Res. 14: 793-803.
Gilbert C., Ropiquet A., Hassanin A. Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): systematics, morphology and biogeography. Mol. Phylogenet. Evol. 40: 101-118.