A. B-ezier, Polydnaviruses of braconid wasps derive from an ancestral nudivirus, dynamics of bracoviruses, vol.368, pp.926-930, 1626.

G. R. Burke and N. A. Moran, Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids, Genome Biol Evol, vol.3, pp.195-208, 2011.

G. R. Burke, S. A. Thomas, J. H. Eum, and M. R. Strand, Mutualistic polydnaviruses share essential replication gene functions with pathogenic ancestors, PLoS Pathog, vol.9, issue.5, p.1003348, 2013.

G. R. Burke, T. J. Simmonds, S. A. Thomas, and M. R. Strand, Microplitis demolitor bracovirus proviral loci and clustered replication genes exhibit distinct DNA amplification patterns during replication, J Virol, vol.89, issue.18, pp.9511-9523, 2015.

G. R. Burke, K. K. Walden, J. B. Whitfield, H. M. Robertson, and M. R. Strand, Widespread genome reorganization of an obligate virus mutualist, PLoS Genet, vol.10, issue.9, p.1004660, 2014.

X. Chen, The sequence of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus genome, J Gen Virol, vol.82, issue.1, pp.241-257, 2001.

R. L. Cheng, Brown planthopper nudivirus DNA integrated in its host genome, J Virol, vol.88, issue.10, pp.5310-5318, 2014.

G. Chevignon, Functional annotation of Cotesia congregata bracovirus: identification of the viral genes expressed in parasitized host immune tissues, J Virol, vol.88, issue.16, pp.8795-8812, 2014.

D. Colinet, A. Schmitz, D. Depoix, D. Crochard, P. et al., Convergent use of RhoGAP toxins by eukaryotic parasites and bacterial pathogens, PLoS Pathog, vol.3, issue.12, p.203, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02337684

A. M. Crawford and C. Sheehan, Replication of oryctes baculovirus in cell culture: viral morphogenesis, infectivity and protein synthesis, J Gen Virol, vol.66, issue.3, pp.529-539, 1985.

J. O. Danquah, S. Botchway, A. Jeshtadi, and L. A. King, Direct interaction of baculovirus capsid proteins VP39 and EXON0 with kinesin-1 in insect cells determined by fluorescence resonance energy transferfluorescence lifetime imaging microscopy, J Virol, vol.86, issue.2, pp.844-853, 2012.

W. Ding, L. Lin, B. Chen, and J. Dai, L1 elements, processed pseudogenes and retrogenes in mammalian genomes, IUBMB Life, vol.58, issue.12, pp.677-685, 2006.

F. Dong, J. Wang, R. Deng, and X. Wang, Autographa californica multiple nucleopolyhedrovirus gene ac81 is required for nucleocapsid envelopment, Virus Res, vol.221, pp.47-57, 2016.

J. M. Drezen, E. A. Herniou, B. , and A. , Evolutionary progenitors of bracoviruses, Parasitoid viruses symbionts and pathogens, pp.15-31, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00780036

J. M. Drezen, Endogenous viruses of parasitic wasps: variations on a common theme, Curr Opin Virol, vol.25, pp.41-48, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01605633

M. S. Dushay and N. E. Beckage, Dose-dependent separation of Cotesia congregata associated polydnavirus effects on Manduca sexta larval development and immunity, J. Insect Physiol, vol.39, issue.12, pp.1029-1040, 1993.

I. Feddersen, K. Sanders, and O. Schmidt, Virus-like particles with host protein-like antigenic determinants protect an insect parasitoid from encapsulation, Experientia, vol.42, pp.1278-1281, 1986.

C. Feschotte and C. Gilbert, Endogenous viruses: insights into viral evolution and impact on host biology, Nat Rev Genet, vol.13, issue.4, pp.283-296, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00679842

M. P. Francino, An adaptive radiation model for the origin of new gene functions, Nat Genet, vol.37, issue.6, pp.573-577, 2005.

J. A. Frank and C. Feschotte, Co-option of endogenous viral sequences for host cell function, Curr Opin Virol, vol.25, pp.81-89, 2017.

J. Gauthier, J. M. Drezen, and E. A. Herniou, Forthcoming 2017. The recurrent domestication of viruses: major evolutionary transitions in parasitic wasps, Parasitology 1, p.13

L. A. Guarino, B. Xu, J. J. Dong, and W. , A virus-encoded RNA polymerase purified from baculovirus-infected cells, J Virol, vol.72, issue.10, pp.7985-7991, 1998.

D. Gundersen-rindal, C. Dupuy, E. Huguet, and J. M. Drezen, Parasitoid Polydnaviruses: evolution, pathology and applications, Biocontrol Sci Technol, vol.23, issue.1, pp.1-61, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00860182

T. A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucl Acids Symp Ser, vol.41, pp.95-98, 1999.

A. Heddi, A. M. Grenier, C. Khatchadourian, H. Charles, and P. Nardon, Four intracellular genomes direct weevil biology: nuclear, mitochondrial, principal endosymbiont, and Wolbachia, Proc Natl Acad Sci, vol.96, issue.12, pp.6814-6819, 1999.

C. C. Hentschel and M. L. Birnstiel, The organization and expression of histone gene families, Cell, vol.25, issue.2, pp.301-313, 1981.

E. A. Herniou, J. A. Olszewski, J. S. Cory, O. Reilly, and D. R. , The genome sequence and evolution of baculoviruses, Annu Rev Entomol, vol.48, pp.211-234, 2003.

T. Hill and R. L. Unckless, The dynamic evolution of Drosophila innubila nudivirus, Infect Genet Evol, vol.57, pp.151-157, 2018.

E. C. Holmes, The evolution of endogenous viral elements, Cell Host Microbe, vol.10, issue.4, pp.368-377, 2011.

Z. H. Hu, Distinct gene arrangement in the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome, J Gen Virol, vol.79, issue.11, pp.2841-2851, 1998.

A. L. Hughes and R. Friedman, Genome-wide survey for genes horizontally transferred from cellular organisms to baculoviruses, Mol Biol Evol, vol.20, issue.6, pp.979-987, 2003.

J. A. Jehle, Creation of a new Family Nudiviridae including two new genera and three species, Taxonomy Poposal, vol.29, 2013.

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res, vol.30, issue.14, pp.3059-3066, 2002.

A. Katzourakis and R. J. Gifford, Endogenous viral elements in animal genomes, PLoS Genet, vol.6, issue.11, p.1001191, 2010.

M. Kearse, Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, vol.28, issue.12, pp.1647-1649, 2012.

C. Labrosse, A RhoGAP protein as a main immune suppressive factor in the Leptopilina boulardi (Hymenoptera, Figitidae)-Drosophila melanogaster interaction, Insect Biochem Mol Biol, vol.35, issue.2, pp.93-103, 2005.

C. Lavialle, Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation, Philos Trans R Soc Lond B Biol Sci, vol.368, p.20120507, 1626.

M. R. Lieber, The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair, Bioessays, vol.19, issue.3, pp.233-240, 1997.

C. L. Lin, Persistent Hz-1 virus infection in insect cells: evidence for insertion of viral DNA into host chromosomes and viral infection in a latent status, J Virol, vol.73, issue.1, pp.128-139, 1999.

F. Louis, The bracovirus genome of the parasitoid wasp Cotesia congregata is amplified within 13 replication units, including sequences not packaged in the particles, J Virol, vol.87, issue.17, pp.9649-9660, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00862145

M. Mangeney, Placental syncytins: genetic disjunction between the fusogenic and immunosuppressive activity of retroviral envelope proteins, Proc Natl Acad Sci, vol.104, issue.51, pp.20534-20539, 2007.

J. P. Mccutcheon and N. A. Moran, Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution, 2010.

, Genome Biol Evol, vol.2, pp.708-718

A. Mira, H. Ochman, and N. A. Moran, Deletional bias and the evolution of bacterial genomes, Trends Genet, vol.17, issue.10, pp.589-596, 2001.

N. A. Moran, Tracing the evolution of gene loss in obligate bacterial symbionts, Curr Opin Microbiol, vol.6, issue.5, pp.512-518, 2003.

N. A. Moran and M. A. , The process of genome shrinkage in the obligate symbiont Buchnera aphidicola, Genome Biol, vol.2, pp.1-12, 2001.

N. A. Moran and G. R. Plague, Genomic changes following host restriction in bacteria, Curr Opin Genet Dev, vol.14, issue.6, pp.627-633, 2004.

N. A. Moran and G. M. Bennett, The tiniest tiny genomes, Annu Rev Microbiol, vol.68, issue.1, pp.195-215, 2014.

M. A. Munson, Evidence for the establishment of aphideubacterium endosymbiosis in an ancestor of four aphid families, J Bacteriol, vol.173, issue.20, pp.6321-6324, 1991.

N. Murphy, J. C. Banks, J. B. Whitfield, and A. D. Austin, Phylogeny of the parasitic microgastroid subfamilies (Hymenoptera: braconidae) based on sequence data from seven genes, with an improved time estimate of the origin of the lineage, Mol Phylogenet Evol, vol.47, issue.1, pp.378-395, 2008.

D. E. Neafsey, Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes, Science, vol.347, issue.6217, p.1258522, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02315921

Z. Nizami, S. Deryusheva, and J. G. Gall, The Cajal body and histone locus body, Cold Spring Harb Perspect Biol, vol.2, issue.7, p.653, 2010.

K. F. Oakeson, Genome degeneration and adaptation in a nascent stage of symbiosis, Genome Biol Evol, vol.6, issue.1, pp.76-93, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01449146

N. Parkinson, C. Conyers, and I. Smith, A venom protein from the endoparasitoid wasp Pimpla hypochondriaca is similar to snake venom reprolysin-type metalloproteases, J Invertebr Pathol, vol.79, issue.2, pp.129-131, 2002.

F. Pasquier-barre, Polydnavirus replication: the EP1 segment of the parasitoid wasp Cotesia congregata is amplified within a larger precursor molecule, J Gen Virol, vol.83, pp.2035-2045, 2002.

E. D. Pastuzyn, The neuronal gene Arc encodes a repurposed retrotransposon Gag protein that mediates intercellular RNA transfer, Cell, vol.172, issue.1-2, pp.275-288, 2018.

K. Peng, M. M. Van-oers, Z. Hu, J. W. Van-lent, and J. M. Vlak, Baculovirus per os infectivity factors form a complex on the surface of occlusionderived virus, J Virol, vol.84, issue.18, pp.9497-9504, 2010.

K. Peng, Characterization of novel components of the baculovirus per os infectivity factor complex, J Virol, vol.86, issue.9, pp.4981-4988, 2012.

A. Pichon, Recurrent DNA virus domestication leading to different parasite virulence strategies, Sci Adv, vol.1, issue.10, p.1501150, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01318262

A. Reineke, S. Asgari, G. Ma, M. Beck, and O. Schmidt, Sequence analysis and expression of a virus-like particle protein, VLP2, from the parasitic wasp Venturia canescens, Insect Mol Biol, vol.11, issue.3, pp.233-239, 2002.

R. V. Rio, G. M. Attardo, and B. L. Weiss, Grandeur alliances: symbiont metabolic integration and obligate arthropod hematophagy, Trends Parasitol, vol.32, issue.9, pp.739-749, 2016.

C. Serbielle, Evolutionary mechanisms driving the evolution of a large polydnavirus gene family coding for protein tyrosine phosphatases, BMC Evol Biol, vol.12, p.253, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00780392

C. Serbielle, Viral cystatin evolution and threedimensional structure modelling: a case of directional selection acting on a viral protein involved in a host-parasitoid interaction, BMC Biol, vol.6, issue.1, p.38, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00324548

S. Shigenobu, H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa, Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp, Nature, vol.407, pp.81-86, 2000.

G. S. Slater and E. Birney, Automated generation of heuristics for biological sequence comparison, BMC Bioinformatics, vol.6, issue.1, p.31, 2005.

W. O. Sparks, R. L. Harrison, and B. C. Bonning, Autographa californica multiple nucleopolyhedrovirus ODV-E56 is a per os infectivity factor, but is not essential for binding and fusion of occlusion-derived virus to the host midgut, Virology, vol.409, issue.1, pp.69-76, 2011.

M. R. Strand, Polydnavirus gene products that interact with the host immune system, Parasitoid viruses symbionts and pathogens, pp.149-161, 2012.

R. E. Tarlinton, J. Meers, and P. R. Young, Retroviral invasion of the koala genome, Nature, vol.442, issue.7098, pp.79-81, 2006.

A. Th-ez-e-j,-b-ezier, G. Periquet, J. M. Drezen, and E. A. Herniou, Paleozoic origin of insect large dsDNA viruses, Proc Natl Acad Sci, vol.108, issue.38, pp.15931-15935, 2011.

, Virus Domestication Involves Specific Pseudogenization in Venturia canescens Genome GBE

, Genome Biol. Evol, vol.10, issue.7, pp.1745-1764, 2018.

J. Th-ez-e, J. Takatsuka, M. Nakai, B. Arif, and E. A. Herniou, Gene acquisition convergence between entomopoxviruses and baculoviruses. Viruses, vol.7, pp.1960-1974, 2015.

A. L. Vanarsdall, K. Okano, and G. F. Rohrmann, Characterization of the role of very late expression factor 1 in baculovirus capsid structure and DNA processing, J Virol, vol.80, issue.4, pp.1724-1733, 2006.

A. N. Volkoff, Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome, PLoS Pathog, vol.6, issue.5, p.1000923, 2010.
URL : https://hal.archives-ouvertes.fr/inria-00537901

M. Wang, Specificity of baculovirus P6.9 basic DNA-binding proteins and critical role of the C terminus in virion formation, J Virol, vol.84, issue.17, pp.8821-8828, 2010.

Y. Wang and J. A. Jehle, Nudiviruses and other large, double-stranded circular DNA viruses of invertebrates: new insights on an old topic, J Invert Pathol, vol.101, issue.3, pp.187-193, 2009.

Y. Wang, O. Bininda-emonds, and J. A. Jehle, Viral genomesmolecular structure, diversity, gene expression mechanisms and host-virus interactions, 2012.

Y. Wang, R. G. Kleespies, A. M. Huger, and J. A. Jehle, The genome of Gryllus bimaculatus nudivirus indicates an ancient diversification of baculovirus-related nonoccluded nudiviruses of insects, J Virol, vol.81, issue.10, pp.5395-5406, 2007.

Y. Wang, O. R. Bininda-emonds, M. M. Van-oers, J. M. Vlak, and J. A. Jehle, The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-stranded DNA viruses, Virus Genes, vol.42, issue.3, pp.444-456, 2011.

C. L. Webster, The discovery, distribution, and evolution of viruses associated with Drosophila melanogaster, PLoS Biol, vol.13, issue.7, p.1002210, 2015.

J. J. Wernegreen, Genome evolution in bacterial endosymbionts of insects, Nat Rev Genet, vol.3, issue.11, pp.850-861, 2002.

C. Wetterwald, Identification of bracovirus particle proteins and analysis of their transcript levels at the stage of virion formation, J Gen Virol, vol.91, pp.2610-2619, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00551409

J. B. Whitfield, A. D. Austin, and J. L. Fernandez-triana, Systematics, biology, and evolution of Microgastrine Parasitoid Wasps, Annu Rev Entomol, vol.63, issue.1, pp.389-406, 2018.

W. Wu, Autographa californica multiple nucleopolyhedrovirus 38K is a novel nucleocapsid protein that interacts with VP1054, VP39, VP80, and itself, J Virol, vol.82, issue.24, pp.12356-12364, 2008.

T. Wyler and B. Lanzrein, Ovary development and polydnavirus morphogenesis in the parasitic wasp Chelonus inanitus. II. Ultrastructural analysis of calyx cell development, virion formation and release, J Gen Virol, vol.84, pp.1151-1163, 2003.

J. Xiao, Pseudogenes and their genome-wide prediction in plants, Int J Mol Sci, vol.17, issue.12, 1991.

Z. Zhang, P. M. Harrison, Y. Liu, and M. Gerstein, Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome, Genome Res, vol.13, issue.12, pp.2541-2558, 2003.