Jonathan, Filée

Permanent Researcher (CR1), CNRS.
Equipe Elements Génétiques Mobiles (ELEGEM)

Tèl. 33 1 69 82 37 05
Fax 33 1 69 82 37 36


Evolutionnary genomics of Viruses and Transposons

Viruses are ubiquitous components of the biosphere and their number exceeds that of cells by at least an order of magnitude. This abundance is also accompanied by an extraordinary diversity in genome size, composition and organisation and viruses have been divided into many different classes based on these criteria. These observations raise multiple questions about the origin and evolution of different viral classes.

My researches focus on the diversity and genome evolution of various classes of mobile elements including large DNA viruses and phages, Retroviruses/Retrotransposons and DNA transposons. I’m also interested by the evolutionary relationships between these elements and their cellular hosts i.e. lateral gene exchange and exaptation of viral genes to accomplish cellular processes.

Curriculum vitae

2000 : DEA « Biodiversité : Génétique, Histoire et Mécanisme de l’évolution », Université Paris XI Orsay (France).
2000-2003 : PhD degree, Université Paris XI Orsay (France), IGM (Patrick Forterre Lab).
2003-2007 : Postdoc, Université Toulouse III (France), LMGM (Henry Krisch and Mick Chandler Labs).
2007- : Permanent Researcher (CR), CNRS, LEGS


Disdero, E. & J. Filée (2017) LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences. Mobile DNA, 8, 6. 10.1186/s13100-017-0088-x.

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. 15;16(1):1061

Filée J (2015). Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution. Front Microbiol. 16;6:593

Filée J. (2014)  Multiple occurrences of Giant Virus core genes acquired by Eukaryotic genomes: the visible part of the iceberg ? Virology. ;466-467:53-9.

Kamoun C, Payen T, Hua-Van A, Filée J. (2013) Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods. BMC Genomics 11;14:700

Filée J. (2013) Route of NCLDV evolution: the genomic accordion. Curr Opin Virol. 3(5):595-9

Metcalfe CJ, Filée J, Germon I, Joss J, Casane D. (2012) Mode and tempo in inflation of size of the Australian lungfish (Neoceratodus forsteri) genome: a major role for CR1-like elements. Mol. Biol. Evol. 9(11):3529-39

Hua-Van A, Le Rouzic A, Boutin TS, Filée J, Capy P. (2011) The struggle for life of the genome’s selfish architects. Biol. Direct 6:19..

Filée J, Chandler M. (2010) Gene exchange and the origin of Giant Viruses. Intervirology 53(5):354-61.

Rouault JD, Casse N, Chénais B, Hua-Van A, Filée J, Capy P (2009) Automatic classification within families of transposable elements: application to the mariner Family. Gene.15;448(2):227-32.

Filée J (2009) Lateral gene transfer, lineage-specific gene expansion and the evolution of Nucleo Cytoplasmic Large DNA viruses.J Invertebr Pathol. 101(3):169-71

Filée J, Pouget N, Chandler M. (2008) Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic Large DNA Viruses.BMC Evol Biol. 26;8:320

Filee J, Siguier P, Chandler M (2007) Insertion Sequence diversity in Archaea. Microbiol Mol Biol Rev. 71(1):121-57

Filee J, Siguier P, Chandler M (2007) I am what I eat and I eat what I am: acquisition of bacterial genes by Giant Viruses. Trends Genet. 23(1):10-5

Siguier P, Filee J, Chandler M (2006) Insertion Sequences in Prokaryotic Genomes. Curr. Opin. Microbiol. 9(5):526-31

Filee J, Bapteste E, Susko E, Krisch HM (2006) A Selective Barrier to Horizontal Gene Transfer in the T4-Type Bacteriophages that Has Preserved a Core Genome with the Viral Replication and Structural Genes. Mol. Biol. Evol. 23(9):1688-1696

Filee J, Comeau AM, Suttle CA, Krisch HM (2006) T4-type bacteriophages. Med Sci. 22(2):111-2.

Filee J, Tetart F, Suttle CA, Krisch HM (2005) Marine T4-type bacteriophages, a ubiquitous component of the dark Matter of the biosphere. Proc.Natl.Acad.Sci.USA. 102(35):12471-6

Filee J, Forterre P (2005) Viral proteins functioning in organelles: a cryptic origin? Trends Microbiol. 13(11):510-3

Filee J, Forterre P, Laurent J (2003) The role played by viruses on the Evolution of their cellular host: a view on informational proteins phylogenies. Res. Microbiol. 154:237-43

Myllykallio H, Leduc D, Filee J, Liebl U (2003) Life without dihydrofolate reductase FolA. Trends Microbiol. 11(5):220-3

Gadelle D, Filee J, Buhler C, Forterre P (2003) Phylogenomics of type II DNA topoisomerases. BioEssay 25: 232-242.

Myllykallio H, Lipowsky G, Leduc D, Filee J, Forterre P, Liebl U (2002) An alternative flavin-dependent mechanism for thymidylate synthesis. Science 5578:105-7.

Filee J, Forterre P, Sen-Lin T, Laurent J (2002) Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J Mol Evol 54:763-73.