L. M. Iyer, S. Balaji, E. V. Koonin, and L. Aravind, Evolutionary genomics of nucleo-cytoplasmic large DNA viruses, CrossRef] [PubMed] 2. Koonin, E.V.; Yutin, N. Nucleo-cytoplasmic Large DNA Viruses (NCLDV) of Eukaryotes, pp.156-184, 2006.
DOI : 10.1016/j.virusres.2006.01.009

N. Philippe, M. Legendre, G. Doutre, Y. Couté, O. Poirot et al., Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes Giant viruses come of age Counts and sequences, observations that continue to change our understanding of viruses in nature, Science Curr. Opin. Microbiol. J. Microbiol. Seoul Korea, vol.341, issue.53, pp.281-286, 2013.
URL : https://hal.archives-ouvertes.fr/cea-00862677

P. Hingamp, N. Grimsley, S. G. Acinas, C. Clerissi, L. Subirana et al., Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes Linking Virus Genomes with Host Taxonomy, CrossRef] [PubMed] 8. Blanc, G.; Gallot-Lavallée, L.; Maumus, F. Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses. Proc. Natl. Acad. Sci. USA 2015, pp.1678-1695, 2016.

F. Maumus, A. Epert, F. Nogué, and G. Blanc, Plant genomes enclose footprints of past infections by giant virus relatives, Nature Communications, vol.5, issue.1, 2014.
DOI : 10.1111/j.1751-1097.1983.tb03388.x
URL : https://hal.archives-ouvertes.fr/hal-01204072

V. Sharma, P. Colson, R. Giorgi, P. Pontarotti, and D. Raoult, DNA-Dependent RNA Polymerase Detects Hidden Giant Viruses in Published Databanks, Genome Biology and Evolution, vol.6, issue.7, pp.1603-1610
DOI : 10.1186/1743-422X-6-223
URL : https://hal.archives-ouvertes.fr/hal-01308942

L. Wang, S. Wu, T. Liu, J. Sun, S. Chi et al., Endogenous viral elements in algal genomes, Acta Oceanologica Sinica, vol.17, issue.9, pp.102-107, 2014.
DOI : 10.1093/bioinformatics/17.9.847

N. Delaroque and W. Boland, The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses, BMC Evolutionary Biology, vol.8, issue.1, p.110, 2008.
DOI : 10.1186/1471-2148-8-110

J. Filée, Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: The visible part of the iceberg?, Virology, vol.466, issue.467, pp.466-467
DOI : 10.1016/j.virol.2014.06.004

R. H. Meints, R. G. Ivey, A. M. Lee, and T. Choi, Identification of Two Virus Integration Sites in the Brown Alga Feldmannia Chromosome, Journal of Virology, vol.82, issue.3, pp.1407-1413, 2008.
DOI : 10.1128/JVI.01983-07

N. Delaroque, I. Maier, R. Knippers, and D. G. Müller, Persistent virus integration into the genome of its algal host, Ectocarpus siliculosus (Phaeophyceae)., Journal of General Virology, vol.80, issue.6, pp.1367-1370, 1999.
DOI : 10.1099/0022-1317-80-6-1367

F. Maumus and G. Blanc, Study of gene trafficking between Acanthamoeba and giant viruses suggests an undiscovered family of amoeba-infecting viruses, Genome Biol. Evol, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01768349

N. Yutin, Y. I. Wolf, D. Raoult, and E. Koonin, Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution, Virology Journal, vol.6, issue.1, p.223, 2009.
DOI : 10.1186/1743-422X-6-223

. Available-online, , 2016.

, Available online: https://www.bioinfodata.org, Blast4OneKP, 2016.

. Available-online, , 2016.

. Available-online, Callum_FINAL_biosample_ids.xls, vol.104, 2016.

. Available-online, , 2016.

N. Yutin, D. Raoult, and E. Koonin, Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies, Virology Journal, vol.10, issue.1, p.158, 2013.
DOI : 10.1080/10635150390235520

A. Dereeper, S. Audic, J. Claverie, and G. Blanc, BLAST-EXPLORER helps you building datasets for phylogenetic analysis, BMC Evolutionary Biology, vol.10, issue.1, 2010.
DOI : 10.1186/1471-2148-10-8

K. Katoh, K. Kuma, H. Toh, and T. Miyata, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Research, vol.33, issue.2, pp.511-518, 2005.
DOI : 10.1093/nar/gki198

M. N. Price, P. S. Dehal, and A. Arkin, FastTree 2 ??? Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, issue.3, 2010.
DOI : 10.1371/journal.pone.0009490.s003

P. J. Keeling, F. Burki, H. M. Wilcox, B. Allam, and E. E. Allen,

J. M. Archibald, A. K. Bharti, and C. J. Bell, The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing, PLoS Biol, vol.12, p.1001889, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01109521

N. Matasci, L. Hung, Z. Yan, E. J. Carpenter, N. J. Wickett et al.,

S. Ayyampalayam and M. Barker, Data access for the 1,000 Plants (1KP) project, GigaScience, vol.2014, issue.3, p.17

S. Suzuki, K. Ishida, and Y. Hirakawa, Diurnal transcriptional regulation of endosymbiotically derived genes in the chlorarachniophyte Bigelowiella natans, Genome Biol. Evol, 2016.

J. S. Park, B. C. Cho, and A. G. Simpson, Halocafeteria seosinensis gen. et sp. nov. (Bicosoecida), a halophilic bacterivorous nanoflagellate isolated from a solar saltern. Extrem. Life Extreme Cond, pp.493-504, 2006.

M. G. Fischer, M. J. Allen, W. H. Wilson, and C. A. Suttle, Giant virus with a remarkable complement of genes infects marine zooplankton, Proc. Natl. Acad. Sci. USA 2010, pp.19508-19513
DOI : 10.1101/gr.6358607

M. G. Fischer and C. A. Suttle, A Virophage at the Origin of Large DNA Transposons, Science, vol.6, issue.11, pp.231-234, 2011.
DOI : 10.1371/journal.pgen.1001210

J. L. Van-etten and D. D. Dunigan, Chloroviruses: not your everyday plant virus, Trends in Plant Science, vol.17, issue.1, pp.1-8
DOI : 10.1016/j.tplants.2011.10.005

C. Clerissi, N. Grimsley, H. Ogata, P. Hingamp, J. Poulain et al., ABSTRACT, Applied and Environmental Microbiology, vol.80, issue.10, pp.3150-3160, 2014.
DOI : 10.1128/AEM.00123-14

W. H. Wilson, J. L. Van-etten, and M. J. Allen, The Phycodnaviridae: The Story of How Tiny Giants Rule the World, Curr. Top. Microbiol. Immunol, vol.328, pp.1-42, 2009.
DOI : 10.1007/978-3-540-68618-7_1

L. A. Hanson, M. R. Rudis, M. Vasquez-lee, and R. D. Montgomery, A broadly applicable method to characterize large DNA viruses and adenoviruses based on the DNA polymerase gene, Virology Journal, vol.3, issue.1, p.28, 2006.
DOI : 10.1186/1743-422X-3-28

F. Chen and C. A. Suttle, Evolutionary Relationships among Large Double-Stranded DNA Viruses That Infect Microalgae and Other Organisms as Inferred from DNA Polymerase Genes, Virology, vol.219, issue.1, pp.170-178, 1996.
DOI : 10.1006/viro.1996.0234

M. Takemura, S. Yokobori, and H. Ogata, Evolution of Eukaryotic DNA Polymerases via Interaction Between Cells and Large DNA Viruses, Journal of Molecular Evolution, vol.1, issue.1-2, pp.24-33, 2015.
DOI : 10.1016/j.coviro.2011.05.008

N. Yutin and E. Koonin, Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes, Virology Journal, vol.9, issue.1, p.161
DOI : 10.1186/1743-422X-9-161

N. Yutin, P. Colson, D. Raoult, and E. V. Koonin, Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family, Virology Journal, vol.10, issue.1, p.106, 2013.
DOI : 10.1186/1743-422X-10-106
URL : https://hal.archives-ouvertes.fr/inserm-00808995

A. M. King, M. J. Adams, E. B. Carstens, and E. J. Lefkowitz, Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses, 2011.

J. K. Colbourne, M. E. Pfrender, D. Gilbert, W. K. Thomas, A. Tucker et al., The Ecoresponsive Genome of Daphnia pulex, Science, vol.3, issue.2, pp.555-561, 2011.
DOI : 10.1101/gr.553803

S. Baumgarten, O. Simakov, L. Y. Esherick, Y. J. Liew, E. M. Lehnert et al., The genome of Aiptasia, a sea anemone model for coral symbiosis, Proc. Natl

. Acad, . Sci, and . Usa, , pp.11893-11898, 2015.

K. Hori, F. Maruyama, T. Fujisawa, T. Togashi, N. Yamamoto et al., et al. Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation, Nat. Commun, vol.5, pp.2014-3978

N. Ye, X. Zhang, M. Miao, X. Fan, Y. Zheng et al., et al. Saccharina genomes provide novel insight into kelp biology, Nat. Commun, vol.6, pp.2015-6986

Y. Chang, S. Wang, S. Sekimoto, A. L. Aerts, C. Choi et al., Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants, Genome Biology and Evolution, vol.278, issue.6, pp.1590-1601, 2015.
DOI : 10.1007/s00438-007-0257-6

J. Filée and M. Chandler, Gene Exchange and the Origin of Giant Viruses, Intervirology, vol.53, issue.5, pp.354-361, 2010.
DOI : 10.1159/000312920

Y. Stram and L. Kuzntzova, Inhibition of Viruses by RNA Interference, Virus Genes, vol.78, issue.Suppl. 1, pp.299-306, 2006.
DOI : 10.3748/wjg.v10.i20.2967

S. Mcqueen-mason, D. M. Durachko, and D. J. Cosgrove, Two Endogenous Proteins That Induce Cell Wall Extension in Plants, THE PLANT CELL ONLINE, vol.4, issue.11, pp.1425-1433, 1992.
DOI : 10.1105/tpc.4.11.1425

N. H. Yennawar, L. Li, D. M. Dudzinski, A. Tabuchi, and D. J. Cosgrove, Crystal structure and activities of EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize, Proc. Natl. Acad. Sci, pp.14664-14671, 2006.
DOI : 10.1074/jbc.M208804200

N. Nikolaidis, N. Doran, and D. J. Cosgrove, Plant Expansins in Bacteria and Fungi: Evolution by Horizontal Gene Transfer and Independent Domain Fusion, Molecular Biology and Evolution, vol.328, issue.2, pp.376-386, 2014.
DOI : 10.1126/science.1187145

J. M. Hardwick, Cyclin' on the viral path to destruction, Nature Cell Biology, vol.10, issue.11, pp.203-204, 2000.
DOI : 10.1016/S0959-437X(99)00045-3

S. Bagga and M. J. Bouchard, Cell Cycle Regulation During Viral Infection, Methods Mol. Biol. Clifton NJ 2014, vol.1170, pp.165-227
DOI : 10.1007/978-1-4939-0888-2_10

S. M. Bowman and S. J. Free, The structure and synthesis of the fungal cell wall, BioEssays, vol.97, issue.8, pp.799-808, 2006.
DOI : 10.1016/S0925-4439(99)00058-7

T. Yamada, H. Onimatsu, and J. L. Van-etten, Chlorella Viruses, Adv. Virus Res, vol.66, pp.293-336, 2006.
DOI : 10.1016/S0065-3527(06)66006-5

T. Klose and M. G. Rossmann, Structure of large dsDNA viruses, Biological Chemistry, vol.395, issue.7-8, pp.711-719
DOI : 10.1515/hsz-2014-0145

M. Legendre, J. Bartoli, L. Shmakova, S. Jeudy, K. Labadie et al., Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology, Proc. Natl. Acad. Sci. USA 2014, pp.4274-4279
DOI : 10.1093/molbev/msr121
URL : https://hal.archives-ouvertes.fr/hal-02193478

S. M. Short, The ecology of viruses that infect eukaryotic algae, Environmental Microbiology, vol.45, issue.9, pp.2253-2271
DOI : 10.3354/ame045001