, People's Republic of China. 10 China National GeneBank, 20560-0165, USA. 4 Data Science Lab, vol.7261, p.34095, 100193.

M. A. Brockhurst, T. Chapman, K. C. King, J. E. Mank, S. Paterson et al., Running with the Red Queen: the role of biotic conflicts in evolution, Proc Biol Sci, vol.281, 2014.

S. L. Nuismer and S. P. Otto, Host-parasite interactions and the evolution of gene expression, PLoS Biol, vol.3, issue.7, p.203, 2005.

J. M. Greenwood, A. L. Ezquerra, S. Behrens, A. Branca, and L. Mallet, Current analysis of host-parasite interactions with a focus on next generation sequencing data, Zoology (Jena), vol.119, issue.4, pp.298-306, 2016.

A. A. Forbes, R. K. Bagley, M. A. Beer, A. C. Hippee, and H. A. Widmayer, Quantifying the unquantifiable: why Hymenoptera, not Coleoptera, is the most speciose animal order, BMC Ecol, vol.18, 2018.

N. E. Beckage and D. B. Gelman, Wasp parasitoid disruption of host development: implications for new biologically based strategies for insect control, Annu Rev Entomol, vol.49, pp.299-330, 2004.

I. Darboux, M. Cusson, and A. N. Volkoff, The dual life of ichnoviruses, Curr Opin Insect Sci, vol.32, pp.47-53, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02124768

M. Turnbull and B. Webb, Perspectives on polydnavirus origins and evolution, Adv Virus Res, vol.58, pp.203-54, 2002.

B. Webb, Polydnavirus biology, genome structure, and evolution, The Insect Viruses, pp.105-144, 1998.

B. Webb and M. R. Strand, The biology and genomics of polydnaviruses, Comprehensive Molecular Insect Science, pp.260-323, 2005.

J. B. Whitfield, Molecular and morphological data suggest a single origin of the polydnaviruses among braconid wasps, Naturwissenschaften, vol.84, issue.11, pp.502-509, 1997.

J. B. Whitfield, Estimating the age of the polydnavirus/braconid wasp symbiosis, P Natl Acad Sci USA, vol.99, issue.11, pp.7508-7521, 2002.

E. Belle, N. E. Beckage, J. Rousselet, M. Poirie, F. Lemeunier et al., Visualization of polydnavirus sequences in a parasitoid wasp chromosome, J Virol, vol.76, issue.11, pp.5793-5799, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02676601

J. G. Fleming and M. D. Summers, Polydnavirus DNA is integrated in the DNA of its parasitoid wasp host, Proc Natl Acad Sci U S A, vol.88, issue.21, pp.9770-9774, 1991.

M. R. Strand and G. R. Burke, d Polydnaviruses: nature's genetic engineers, Annu Rev Virol, vol.1, pp.333-54, 2014.

A. Bezier, F. Louis, S. Jancek, G. Periquet, J. Theze et al., Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata: insights into the evolutionary dynamics of bracoviruses, Philos Trans R Soc Lond Ser B Biol Sci, vol.368, p.20130047, 1626.
URL : https://hal.archives-ouvertes.fr/hal-00862670

A. N. Volkoff, V. Jouan, S. Urbach, S. Samain, M. Bergoin et al., 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

A. Bezier, M. Annaheim, J. Herbiniere, C. Wetterwald, G. Gyapay et al., Polydnaviruses of braconid wasps derive from an ancestral nudivirus, Science, vol.323, issue.5916, pp.926-956, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00402741

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.378-95, 2008.

J. J. Rodriguez, J. Fernández-triana, M. A. Smith, D. H. Janzen, W. Hallwachs et al., Extrapolations from field studies and known faunas converge on dramatically increased estimates of global microgastrine parasitoid wasp species richness (Hymenoptera: Braconidae), Insect Conserv Divers, vol.6, issue.4, pp.530-536, 2013.

C. Beliveau, A. Cohen, D. Stewart, G. Periquet, A. Djoumad et al., Genomic and proteomic analyses indicate that Banchine and Campoplegine Polydnaviruses have similar, if not identical, Viral Ancestors, J Virol, vol.89, issue.17, pp.8909-8930, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01315371

D. Quicke, The Braconid and Ichneumonid parasitoid wasps: biology, systematics, evolution and ecology, 2015.

A. Pichon, A. Bezier, S. Urbach, J. M. Aury, V. Jouan et al., 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

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.

M. R. Strand and G. R. Burke, Polydnaviruses: from discovery to current insights, Virology, vol.479, pp.393-402, 2015.

L. Cui and B. A. Webb, Homologous sequences in the Campoletis sonorensis polydnavirus genome are implicated in replication and nesting of the W segment family, J Virol, vol.71, issue.11, pp.8504-8517, 1997.

S. Savary, N. Beckage, F. Tan, G. Periquet, and J. M. Drezen, Excision of the polydnavirus chromosomal integrated EP1 sequence of the parasitoid wasp Cotesia congregata (Braconidae, Microgastinae) at potential recombinase binding sites, J Gen Virol, vol.78, pp.3125-3159, 1997.

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

G. R. Burke and M. R. Strand, Deep sequencing identifies viral and wasp genes with potential roles in replication of Microplitis demolitor Bracovirus, J Virol, vol.86, issue.6, pp.3293-306, 2012.

C. A. Desjardins, D. E. Gundersen-rindal, J. B. Hostetler, L. J. Tallon, D. W. Fadrosh et al., Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps, Genome Biol, vol.9, issue.12, p.183, 2008.

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.9511-9534, 2015.

G. R. Burke, K. Walden, J. B. Whitfield, H. M. Robertson, and M. R. Strand, Whole Genome Sequence of the Parasitoid Wasp Microplitis demolitor That Harbors an Endogenous Virus Mutualist. G3 (Bethesda), vol.8, pp.2875-80, 2018.

F. Louis, A. Bezier, G. Periquet, C. Ferras, J. M. Drezen et al., 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.9649-60, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00862145

M. Annaheim and B. Lanzrein, Genome organization of the Chelonus inanitus polydnavirus: excision sites, spacers and abundance of proviral and excised segments, J Gen Virol, vol.88, issue.2, pp.450-457, 2007.

W. Rattanadechakul and B. A. Webb, Characterization of Campoletis sonorensis ichnovirus unique segment B and excision locus structure, J Insect Physiol, vol.49, issue.5, pp.523-555, 2003.

A. Lorenzi, M. Ravallec, M. Eychenne, V. Jouan, S. Robin et al., RNA interference identifies domesticated viral genes involved in assembly and trafficking of virusderived particles in ichneumonid wasps, PLoS Pathog, vol.15, issue.12, p.1008210, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02483831

T. Doremus, F. Cousserans, G. Gyapay, V. Jouan, P. Milano et al., Extensive Transcription Analysis of the Hyposoter didymator Ichnovirus Genome in Permissive and Non-Permissive Lepidopteran Host Species, PLoS One, vol.9, issue.8, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01190108

B. A. Webb, M. R. Strand, S. E. Dickey, M. H. Beck, R. S. Hilgarth et al., Polydnavirus genomes reflect their dual roles as mutualists and pathogens, Virology, vol.347, issue.1, pp.160-74, 2006.

N. I. Weisenfeld, V. Kumar, P. Shah, D. M. Church, and D. B. Jaffe, Direct determination of diploid genome sequences, Genome Res, vol.27, issue.5, pp.757-67, 2017.

R. Kajitani, K. Toshimoto, H. Noguchi, A. Toyoda, Y. Ogura et al., Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

, Genome Res, vol.24, issue.8, pp.1384-95, 2014.

M. Stanke, A. Tzvetkova, and B. Morgenstern, AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome, Genome Biol, vol.7, issue.1, pp.11-11, 2006.

K. J. Hoff, S. Lange, A. Lomsadze, M. Borodovsky, and M. Stanke, BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS, Bioinformatics, vol.32, issue.5, pp.767-776, 2016.

K. R. Bradnam, J. N. Fass, A. Alexandrov, P. Baranay, M. Bechner et al., Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, Gigascience, vol.2, issue.1, p.10, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00868822

S. M. Geib, G. H. Liang, T. D. Murphy, and S. B. Sim, Whole genome sequencing of the Braconid parasitoid wasp Fopius arisanus, an important biocontrol agent of pest Tepritid Fruit Flies. G3 (Bethesda), vol.7, pp.2407-2418, 2017.

E. S. Tvedte, K. Walden, and K. E. Mcelroy, Genome of the parasitoid wasp Diachasma alloeum, an emerging model for ecological speciation and transitions to asexual reproduction, Genome Biol Evol, vol.11, issue.10, pp.2767-73, 2019.

J. H. Werren, S. Richards, C. A. Desjardins, O. Niehuis, J. Gadau et al., Functional and evolutionary insights from the genomes of three parasitoid Nasonia species, Science, vol.327, issue.5963, pp.343-351, 2010.

F. Legeai, B. F. Santos, S. Robin, A. Bretaudeau, R. B. Dikow et al., Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps. BIPAA Hyposoter genome annotation and resources, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02918230

F. Legeai, B. F. Santos, S. Robin, A. Bretaudeau, R. B. Dikow et al., Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps. BIPAA Hyposoter genome annotation and resources, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02918230

F. A. Simao, R. M. Waterhouse, P. Ioannidis, E. V. Kriventseva, and E. M. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, pp.3210-3212, 2015.

B. Paten, D. Earl, N. Nguyen, M. Diekhans, D. Zerbino et al., Cactus: algorithms for genome multiple sequence alignment, Genome Res, vol.21, issue.9, pp.1512-1540, 2011.

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and postanalysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1315, 2014.

J. Y. Yang, X. Chen, A. Mcdermaid, and Q. Ma, DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses, Bioinformatics, vol.33, issue.16, pp.2586-2594, 2017.

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

A. Bennett, S. Cardinal, I. D. Gauld, and D. B. Wahl, Phylogeny of the subfamilies of Ichneumonidae (Hymenoptera), J Hymenopt Res, vol.71, pp.1-156, 2019.

D. Quicke, N. M. Laurenne, M. G. Fitton, and G. R. Broad, A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision, J Nat Hist, vol.43, pp.1305-421, 2009.

M. Cusson, D. Stoltz, R. Lapointe, C. Béliveau, A. Nisole et al., Genomics of banchine ichnoviruses: insights into their relationship to bracoviruses and campoplegine ichnoviruses, Parasitoid viruses: symbionts and pathogens, pp.79-87, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00780045

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.

A. Gruber, P. Stettler, P. Heiniger, D. Schumperli, and B. Lanzrein, Polydnavirus DNA of the braconid wasp Chelonus inanitus is integrated in the wasp's genome and excised only in later pupal and adult stages of the female, J Gen Virol, vol.77, pp.2873-2882, 1996.

C. Serbielle, S. Dupas, E. Perdereau, F. Hericourt, C. Dupuy et al., 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. A. Desjardins, D. E. Gundersen-rindal, J. B. Hostetler, L. J. Tallon, R. W. Fuester et al., Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus, BMC Microbiol, vol.7, p.61, 2007.

C. P. Mézard, D. Pompon, and N. A. , Recombination between similar but not identical DNA sequences during yeast transformation occurs within short stretches of identity, Cell, vol.70, issue.4, pp.659-70, 1992.

M. Jasin and R. Rothstein, Repair of strand breaks by homologous recombination, Cold Spring Harb Perspect Biol, vol.5, issue.11, p.12740, 2013.

R. Bhargava, D. O. Onyango, and J. M. Stark, Regulation of single-strand annealing and its role in genome maintenance, Trends Genet, vol.32, issue.9, pp.566-75, 2016.

B. Elliott, C. Richardson, J. Winderbaum, J. A. Nickoloff, and M. Jasin, Gene conversion tracts from double-strand break repair in mammalian cells, Mol Cell Biol, vol.18, issue.1, pp.93-101, 1998.

M. E. Morales, T. B. White, V. A. Streva, C. B. Defreece, D. J. Hedges et al., The contribution of alu elements to mutagenic DNA double-strand break repair, PLoS Genet, vol.11, issue.3, p.1005016, 2015.

E. B. Rosenblum, C. E. Parent, and E. E. Brandt, The molecular basis of phenotypic convergence, Annu Rev Ecol Evol Syst, vol.45, pp.203-229, 2014.

Y. Hao, Y. Qu, G. Song, and F. Lei, Genomic insights into the adaptive convergent evolution, Curr Genomics, vol.20, issue.2, pp.81-90, 2019.

C. Natarajan, F. G. Hoffmann, R. E. Weber, A. Fago, C. C. Witt et al., Predictable convergence in hemoglobin function has unpredictable molecular underpinnings, Science, vol.354, issue.6310, pp.336-345, 2016.

C. Serbielle, S. Chowdhury, S. Pichon, S. Dupas, J. Lesobre et al., Viral cystatin evolution and three-dimensional structure modelling: a case of directional selection acting on a viral protein involved in a host-parasitoid interaction, BMC Biol, vol.6, p.38, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00324548

M. R. Shaw and K. Horstmann, An analysis of host range in the Diadegma nanus group of parasitoids in Western Europe, with a key to species, J Hymenopt Res, vol.6, pp.273-96, 1997.

M. Frayssinet, P. Audiot, A. Cusumano, A. Pichon, L. E. Malm et al., Western European populations of the Ichneumonid wasp Hyposoter didymator belong to a single taxon, Front Ecol Evol, vol.7, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02446499

H. M. Pacheco, S. L. Vanlaerhoven, M. Garcia, and D. W. Hunt, Food web associations and effect of trophic resources and environmental factors on parasitoids expanding their host range into non-native hosts, Entomol Exp Appl, vol.166, issue.4, pp.277-88, 2018.

P. J. Krell, M. D. Summers, and S. B. Vinson, Virus with a multipartite superhelical DNA genome from the Ichneumonid parasitoid Campoletis sonorensis, J Virol, vol.43, issue.3, pp.859-70, 1982.

B. J. Walker, T. Abeel, T. Shea, M. Priest, A. Abouelliel et al., Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement, PLoS One, vol.9, issue.11, p.112963, 2014.

D. E. Wood, J. Lu, and B. Langmead, Improved metagenomic analysis with Kraken 2, Genome Biol, vol.20, issue.1, p.257, 2019.

W. J. Kent, BLAT--the BLAST-like alignment tool, Genome Res, vol.12, issue.4, pp.656-64, 2002.

R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang et al., SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, Gigascience, vol.1, issue.1, p.18, 2012.

T. Doremus, S. Urbach, V. Jouan, F. Cousserans, M. Ravallec et al., Venom gland extract is not required for successful parasitism in the polydnavirusassociated endoparasitoid Hyposoter didymator (Hym. Ichneumonidae) despite the presence of numerous novel and conserved venom proteins, Insect Biochem Mol Biol, vol.43, issue.3, pp.292-307, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01837249

F. Legeai, B. F. Santos, S. Robin, A. Bretaudeau, R. B. Dikow et al., Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps, Supplementary Datasets. BIPAA Archive, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02918230

T. D. Wu and C. K. Watanabe, GMAP: a genomic mapping and alignment program for mRNA and EST sequences, Bioinformatics, vol.21, issue.9, pp.1859-75, 2005.

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, issue.1, pp.15-21, 2013.

D. Kim, G. Pertea, C. Trapnell, H. Pimentel, R. Kelley et al., TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol, vol.14, issue.4, p.36, 2013.

N. A. Dunn, D. R. Unni, C. Diesh, M. Munoz-torres, N. L. Harris et al., Apollo: democratizing genome annotation, PLoS Comput Biol, vol.15, issue.2, p.1006790, 2019.

T. Flutre, E. Duprat, C. Feuillet, and H. Quesneville, Considering transposable element diversification in de novo annotation approaches, PLoS One, vol.6, issue.1, p.16526, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00568705

H. Quesneville, C. M. Bergman, O. Andrieu, D. Autard, D. Nouaud et al., Combined evidence annotation of transposable elements in genome sequences, PLoS Comput Biol, vol.1, issue.2, pp.166-75, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00009013

N. C. Sheffield and C. Bock, LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor, Bioinformatics, vol.32, issue.4, p.5874589, 2016.

A. R. Quinlan, BEDTools: The Swiss-Army Tool for Genome Feature Analysis, Curr Protoc Bioinformatics, vol.47, pp.11-12, 2014.

D. M. Emms and S. Kelly, OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy

, Genome Biol, vol.16, p.157, 2015.

G. Drillon, A. Carbone, and G. Fischer, SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes, PLoS One, vol.9, issue.3, p.92621, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01358096

J. Rocher, M. Ravallec, P. Barry, A. N. Volkoff, D. Ray et al., Establishment of cell lines from the wasp Hyposoter didymator (Hym., Ichneumonidae) containing the symbiotic polydnavirus H didymator ichnovirus, J Gen Virol, vol.85, pp.863-871, 2004.

A. N. Volkoff, P. Cerutti, J. Rocher, M. Ohresser, G. Devauchelle et al., Related RNAs in lepidopteran cells after in vitro infection with Hyposoter didymator virus define a new polydnavirus gene family, Virology, vol.263, issue.2, pp.349-63, 1999.
URL : https://hal.archives-ouvertes.fr/hal-02694329

F. Legeai, B. F. Santos, S. Robin, A. Bretaudeau, R. B. Dikow et al., Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps, Supplementary Datasets. BIPAA Archi, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02918230

C. Baudet, C. Lemaitre, Z. Dias, C. Gautier, E. Tannier et al., Cassis: detection of genomic rearrangement breakpoints, Bioinformatics, vol.26, issue.15, pp.1897-1905, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00681095

C. Lemaitre, E. Tannier, C. Gautier, and M. F. Sagot, Precise detection of rearrangement breakpoints in mammalian chromosomes, BMC Bioinformatics, vol.9, p.286, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00278553

F. Legeai, B. F. Santos, S. Robin, A. Bretaudeau, R. B. Dikow et al., Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02918230

F. Legeai, B. F. Santos, S. Robin, A. Bretaudeau, R. B. Dikow et al., Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps, p.590982
URL : https://hal.archives-ouvertes.fr/hal-02918230

, Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations