33. Iyer LM, Koonin EV, Leipe DD, Aravind L. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res. 2005 Jul 15; 33(12):3875-96. https://doi.org/10.1093/nar/gki702 PMID: 16027112.

34. Burke GR, Hines HM, Sharanowski BJ. The presence of ancient core genes reveals endogenization from diverse viral ancestors in parasitoid wasps. Genome Biol Evol. 2021 Jul 6; 13(7):evab105. https://doi.org/10.1093/gbe/evab105 PMID: 33988720.

35. Marti D, Grossniklaus-Bürgin C, Wyder S, Wyler T, Lanzrein B. Ovary development and polydnavirus morphogenesis in the parasitic wasp *Chelonus inanitus*. I. Ovary morphogenesis, amplification of viral DNA and ecdysteroid titres. J Gen Virol. 2003 May; 84(Pt 5):1141-1150. https://doi.org/10.1099/vir.0.18832-0

36. Wyler T, Lanzrein B. 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. 2003; 84:1151-63. https://doi.org/10.1099/vir.0.18830-0

37. Baran N, Neer A, Manor H. "Onion skin" replication of integrated polyoma virus DNA and flanking sequences in polyoma-transformed rat cells: termination within a specific cellular DNA segment. Proc Natl Acad Sci U S A. 1983 Jan; 80(1):105-9. https://doi.org/10.1073/pnas.80.1.105 PMID: 6296858

38. Spradling AC. The organization and amplification of two chromosomal domains containing *Drosophila* chorion genes. Cell. 1981 Nov; 27(1 Pt 2):193-201. https://doi.org/10.1016/0092-8674(81)90373-1 PMID: 6799210

39. Kim JC, Nordman J, Xie F, Kashevsky H, Eng T, Li S, et al. Integrative analysis of gene amplification in *Drosophila* follicle cells: parameters of origin activation and repression. Genes Dev. 2011 Jul 1; 25(13):1384-98. https://doi.org/10.1101/gad.2043111 PMID: 21724831

40. Tower J. Developmental gene amplification and origin regulation. Annu Rev Genet. 2004; 38:273-304. https://doi.org/10.1146/annurev.genet.37.110801.143851 PMID: 15568978

41. Foulk MS, Urban JM, Casella C, Gerbi SA. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res. 2015 May; 25(5):725-35. https://doi.org/10.1101/gr.183848.114 PMID: 25695952

42. Burke GR, Simmonds TJ, Thomas SA, Strand MR. *Microplitis demolitor* Bracovirus proviral loci and clustered replication genes exhibit distinct DNA amplification patterns during replication. J Virol. 2015 Sep; 89(18):9511-23. https://doi.org/10.1128/JVI.01388-15 PMID: 26157119

43. Weller SK, Kuchta RD. The DNA helicase-primase complex as a target for herpes viral infection. Expert Opin Ther Targets. 2013 Oct; 17(10):1119-32. https://doi.org/10.1517/14728222.2013.827663 PMID: 23930666

44. Burke GR, Walden KK, Whitfield JB, Robertson HM, Strand MR. Widespread genome reorganization of an obligate virus mutualist. PLoS Genet. 2014 Sep; 10(9):e1004660. https://doi.org/10.1371/journal.pgen.1004660 PMID: 25232843

45. Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, et al. Chromosomal scale assem-
bly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol. 2021 Jan 22; 4
(1):104. Erratum in: Commun Biol. 2021 Jul 30;4(1):940. https://doi.org/10.1038/s42003-020-01623-8
PMID: 33483589

46. Mao M, Strand MR, Burke GR. The complete genome of *Chelonus insularis* reveals dynamic arrangement of genome components in parasitoid wasps that produce bracoviruses. J Virol. 2022 Mar 9; 96(5): e0157321. https://doi.org/10.1128/JVI.01573-21 PMID: 34985997

47. Louis F, Bézier A, Periquet G, Ferras C, Drezen JM, Dupuy C. The bracovirus genome of the parasitoid wasp *Cotesia congregata* is amplified within 13 replication units, including sequences not packaged in the particles. J Virol. 2013 Sep; 87(17):9649-60. https://doi.org/10.1128/JVI.00886-13 PMID: 23804644

48. Visconti V, Eychenne M, Darboux I. Modulation of antiviral immunity by the ichnovirus HdIV in *Spodoptera frugiperda*. Mol Immunol. 2019 Apr; 108:89-101. https://doi.org/10.1016/j.molimm.2019.02.011 PMID: 30784767

49. Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 2016 Mar; 26(3):342-50. https://doi.org/10.1101/gr.193474.115 PMID: 26848124

50. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN].

51. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16; 10(2):giab008. https://doi.org/10.1093/gigascience/giab008 PMID: 33590861
33. Iyer LM, Koonin EV, Leipe DD, Aravind L. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res. 2005 Jul 15; 33(12):3875-96. https://doi.org/10.1093/nar/gki702 PMID: 16027112.

34. Burke GR, Hines HM, Sharanowski BJ. The presence of ancient core genes reveals endogenization from diverse viral ancestors in parasitoid wasps. Genome Biol Evol. 2021 Jul 6; 13(7):evab105. https://doi.org/10.1093/gbe/evab105 PMID: 33988720.

35. Marti D, Grossniklaus-Bürgin C, Wyder S, Wyler T, Lanzrein B. Ovary development and polydnavirus morphogenesis in the parasitic wasp *Chelonus inanitus*. I. Ovary morphogenesis, amplification of viral DNA and ecdysteroid titres. J Gen Virol. 2003 May; 84(Pt 5):1141-1150. https://doi.org/10.1099/vir.0.18832-0

36. Wyler T, Lanzrein B. 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. 2003; 84:1151-63. https://doi.org/10.1099/vir.0.18830-0

37. Baran N, Neer A, Manor H. "Onion skin" replication of integrated polyoma virus DNA and flanking sequences in polyoma-transformed rat cells: termination within a specific cellular DNA segment. Proc Natl Acad Sci U S A. 1983 Jan; 80(1):105-9. https://doi.org/10.1073/pnas.80.1.105 PMID: 6296858

38. Spradling AC. The organization and amplification of two chromosomal domains containing *Drosophila* chorion genes. Cell. 1981 Nov; 27(1 Pt 2):193-201. https://doi.org/10.1016/0092-8674(81)90373-1 PMID: 6799210

39. Kim JC, Nordman J, Xie F, Kashevsky H, Eng T, Li S, et al. Integrative analysis of gene amplification in *Drosophila* follicle cells: parameters of origin activation and repression. Genes Dev. 2011 Jul 1; 25(13):1384-98. https://doi.org/10.1101/gad.2043111 PMID: 21724831

40. Tower J. Developmental gene amplification and origin regulation. Annu Rev Genet. 2004; 38:273-304. https://doi.org/10.1146/annurev.genet.37.110801.143851 PMID: 15568978

41. Foulk MS, Urban JM, Casella C, Gerbi SA. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res. 2015 May; 25(5):725-35. https://doi.org/10.1101/gr.183848.114 PMID: 25695952

42. Burke GR, Simmonds TJ, Thomas SA, Strand MR. *Microplitis demolitor* Bracovirus proviral loci and clustered replication genes exhibit distinct DNA amplification patterns during replication. J Virol. 2015 Sep; 89(18):9511-23. https://doi.org/10.1128/JVI.01388-15 PMID: 26157119

43. Weller SK, Kuchta RD. The DNA helicase-primase complex as a target for herpes viral infection. Expert Opin Ther Targets. 2013 Oct; 17(10):1119-32. https://doi.org/10.1517/14728222.2013.827663 PMID: 23930666

44. Burke GR, Walden KK, Whitfield JB, Robertson HM, Strand MR. Widespread genome reorganization of an obligate virus mutualist. PLoS Genet. 2014 Sep; 10(9):e1004660. https://doi.org/10.1371/journal.pgen.1004660 PMID: 25232843

45. Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, et al. Chromosomal scale assem-
bly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol. 2021 Jan 22; 4
(1):104. Erratum in: Commun Biol. 2021 Jul 30;4(1):940. https://doi.org/10.1038/s42003-020-01623-8
PMID: 33483589

46. Mao M, Strand MR, Burke GR. The complete genome of *Chelonus insularis* reveals dynamic arrangement of genome components in parasitoid wasps that produce bracoviruses. J Virol. 2022 Mar 9; 96(5): e0157321. https://doi.org/10.1128/JVI.01573-21 PMID: 34985997

47. Louis F, Bézier A, Periquet G, Ferras C, Drezen JM, Dupuy C. The bracovirus genome of the parasitoid wasp *Cotesia congregata* is amplified within 13 replication units, including sequences not packaged in the particles. J Virol. 2013 Sep; 87(17):9649-60. https://doi.org/10.1128/JVI.00886-13 PMID: 23804644

48. Visconti V, Eychenne M, Darboux I. Modulation of antiviral immunity by the ichnovirus HdIV in *Spodoptera frugiperda*. Mol Immunol. 2019 Apr; 108:89-101. https://doi.org/10.1016/j.molimm.2019.02.011 PMID: 30784767

49. Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 2016 Mar; 26(3):342-50. https://doi.org/10.1101/gr.193474.115 PMID: 26848124

50. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN].

51. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16; 10(2):giab008. https://doi.org/10.1093/gigascience/giab008 PMID: 33590861
52. Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15; 26(6):841–2. https://doi.org/10.1093/bioinformatics/btq033 PMID: 20110278

53. Liao Y, Smyth GK, Shi W. featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1; 30(7):923–30. https://doi.org/10.1093/bioinformatics/btt656 PMID: 24227677

54. Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, et al. deepTools2: A next-generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016 Jul 8; 44(W1):W160–5. https://doi.org/10.1093/nar/gkw257 PMID: 27079975

55. Bailey TL, Johnson J, Grant CE, Noble WS. The MEME Suite. Nucleic Acids Res. 2015 Jul 1; 43(W1): W39–49. https://doi.org/10.1093/nar/gkv416 PMID: 25953851

56. Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017 Jan 4; 45(D1):D200–D203. https://doi.org/10.1093/nar/gkw1129 PMID: 27899674

57. Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2020 Jan 8; 48(D1):D265–D268. https://doi.org/10.1093/nar/gkz991 PMID: 31777944

58. Thumuluri V, A Armenteros JJ, Johansen AR, Nielsen H, Winther O. DeepLoc 2.0: multi-label subcellular localization prediction using protein language models. Nucleic Acids Research. 2022. https://doi.org/10.1093/nar/gkac278 PMID: 35489069

59. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol. 2021 Jun 25; 38(7):3022–3027. https://doi.org/10.1093/molbev/msab120 PMID: 33892491

60. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2—A multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009; 25:1189–1191. https://doi.org/10.1093/bioinformatics/btp033 PMID: 19151095

61. Gabler F, Nam SZ, Till S, Mirdita M, Steinegger M, Söding J, et al. Protein sequence analysis using the MPI Bioinformatics Toolkit. Curr Protoc Bioinformatics. 2020 Dec; 72(1):e108. https://doi.org/10.1002/cpbi.108 PMID: 33315308

62. Rasband WS. ImageJ. National Institutes of Health, Bethesda, Maryland, USA. 1997–2018. http://imagej.nih.gov/ij

63. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. R Core Team. 2023. URL https://www.R-project.org/.
52. Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15; 26(6):841–2. https://doi.org/10.1093/bioinformatics/btq033 PMID: 20110278

53. Liao Y, Smyth GK, Shi W. featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1; 30(7):923–30. https://doi.org/10.1093/bioinformatics/btt656 PMID: 24227677

54. Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, et al. deepTools2: A next-generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016 Jul 8; 44(W1):W160–5. https://doi.org/10.1093/nar/gkw257 PMID: 27079975

55. Bailey TL, Johnson J, Grant CE, Noble WS. The MEME Suite. Nucleic Acids Res. 2015 Jul 1; 43(W1): W39–49. https://doi.org/10.1093/nar/gkv416 PMID: 25953851

56. Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017 Jan 4; 45(D1):D200–D203. https://doi.org/10.1093/nar/gkw1129 PMID: 27899674

57. Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2020 Jan 8; 48(D1):D265–D268. https://doi.org/10.1093/nar/gkz991 PMID: 31777944

58. Thumuluri V, A Armenteros JJ, Johansen AR, Nielsen H, Winther O. DeepLoc 2.0: multi-label subcellular localization prediction using protein language models. Nucleic Acids Research. 2022. https://doi.org/10.1093/nar/gkac278 PMID: 35489069

59. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol. 2021 Jun 25; 38(7):3022–3027. https://doi.org/10.1093/molbev/msab120 PMID: 33892491

60. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2—A multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009; 25:1189–1191. https://doi.org/10.1093/bioinformatics/btp033 PMID: 19151095

61. Gabler F, Nam SZ, Till S, Mirdita M, Steinegger M, Söding J, et al. Protein sequence analysis using the MPI Bioinformatics Toolkit. Curr Protoc Bioinformatics. 2020 Dec; 72(1):e108. https://doi.org/10.1002/cpbi.108 PMID: 33315308

62. Rasband WS. ImageJ. National Institutes of Health, Bethesda, Maryland, USA. 1997–2018. http://imagej.nih.gov/ij

63. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. R Core Team. 2023. URL https://www.R-project.org/.