C. A. Suttle, Marine viruses-Major players in the global ecosystem, Nat. Rev. Microbiol, vol.5, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01663342

Ø. Bergh, K. Y. Børsheim, G. Bratbak, and M. Heldal, High abundance of viruses found in aquatic environments, Nature, vol.340, pp.467-468, 1989.

C. H. Wigington, D. Sonderegger, C. P. Brussaard, A. Buchan, J. F. Finke et al., Re-examination of the relationship between marine virus and microbial cell abundances, Nat. Microbiol, 2016.

J. A. Fuhrman, Marine viruses and their biogeochemical and ecological effects, Nature, vol.399, pp.541-548, 1999.

F. Rohwer, D. Prangishvili, and D. Lindell, Roles of viruses in the environment, Environ. Microbiol, vol.11, pp.2771-2774, 2009.

R. Danovaro, C. Corinaldesi, A. Dell'anno, J. A. Fuhrman, J. J. Middelburg et al., Marine viruses and global climate change, FEMS Microbiol. Rev, vol.35, pp.993-1034, 2011.

T. Yoshida, Y. Nishimura, H. Watai, N. Haruki, D. Morimoto et al., Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan, ISME J, vol.12, pp.1287-1295, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01771838

L. Guidi, S. Chaffron, L. Bittner, D. Eveillard, A. Larhlimi et al., Plankton networks driving carbon export in the oligotrophic ocean, Nature, vol.532, pp.465-470, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01275276

S. Roux, J. R. Brum, B. E. Dutilh, S. Sunagawa, M. B. Duhaime et al., Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses, Nature, vol.537, pp.689-693, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01376822

Y. Nishimura, H. Watai, T. Honda, T. Mihara, K. Omae et al., Environmental viral genomes shed new light on virus-host interactions in the ocean, vol.2, pp.359-375, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01771841

C. T. Chow and C. A. Suttle, Biogeography of viruses in the sea, Annu. Rev. Virol, vol.2, pp.41-66, 2015.

P. Hingamp, N. Grimsley, S. G. Acinas, C. Clerissi, L. Subirana et al., Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes, ISME J, vol.7, pp.1678-1695, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01258223

Q. Carradec, E. Pelletier, C. Silva, A. Alberti, Y. Seeleuthner et al., A global ocean atlas of eukaryotic genes, Nat. Commun, vol.9, 2018.
URL : https://hal.archives-ouvertes.fr/cea-01874711

D. Arslan, M. Legendre, V. Seltzer, C. Abergel, and J. Claverie, Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae, Proc. Natl. Acad. Sci, vol.108, pp.17486-17491, 2011.

S. Santini, S. Jeudy, J. Bartoli, O. Poirot, M. Lescot et al., Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes, Proc. Natl. Acad. Sci, vol.110, pp.10800-10805, 2013.

T. Mihara, H. Koyano, P. Hingamp, N. Grimsley, S. Goto et al., Taxon richness of "Megaviridae" exceeds those of Bacteria and Archaea in the ocean. Microbes Env, vol.33, pp.162-171, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01978927

J. Claverie, H. Ogata, S. Audic, C. Abergel, K. Suhre et al., Mimivirus and the emerging concept of "giant" virus, Virus Res, vol.117, pp.133-144, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00005228

J. L. Van-etten, Another really, really big virus, vol.3, pp.32-46, 2011.

M. G. Fischer and R. C. Condit, Editorial introduction to "Giant Viruses" special issue of Virology, Virology, pp.466-467, 2014.

L. Gallot-lavallée, G. Blanc, and J. Claverie, Comparative genomics of Chrysochromulina ericina virus and other microalga-infecting large DNA viruses highlights their intricate evolutionary relationship with the established Mimiviridae family, J. Virol, p.91, 2017.

D. Raoult, S. Audic, C. Robert, C. Abergel, P. Renesto et al., The 1.2-Megabase genome sequence of Mimivirus, Science, vol.306, pp.1344-1350, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00651656

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, vol.107, pp.19508-19513, 2010.

M. Moniruzzaman, G. R. Lecleir, C. M. Brown, C. J. Gobler, K. D. Bidle et al., Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host-virus coevolution, Virology, pp.466-467, 2014.

L. Gallot-lavallée, A. Pagarete, M. Legendre, S. Santini, R. Sandaa et al., The 474-kilobase-pair complete genome sequence of CeV-01B, a virus infecting Haptolina (Chrysochromulina) ericina (Prymnesiophyceae), Genome Announc, vol.3, pp.1413-01415, 2015.

P. Colson, X. De-lamballerie, N. Yutin, S. Asgari, Y. Bigot et al., Megavirales", a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses, Arch. Virol, vol.158, pp.2517-2521, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01129809

F. Chen and C. A. Suttle, Amplification of DNA polymerase gene fragments from viruses infecting microalgae, Appl. Environ. Microbiol, vol.61, pp.1274-1278, 1995.

F. Chen, C. A. Suttle, and S. M. Short, Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes, Appl. Environ. Microbiol, vol.62, pp.2869-2874, 1996.

J. B. Larsen, A. Larsen, G. Bratbak, and R. Sandaa, Phylogenetic analysis of members of the Phycodnaviridae virus family, using amplified fragments of the major capsid protein gene, Appl. Environ. Microbiol, vol.74, pp.3048-3057, 2008.

T. V. Johannessen, A. Larsen, G. Bratbak, A. Pagarete, B. Edvardsen et al., Seasonal dynamics of haptophytes and dsDNA algal viruses suggest complex virus-host relationship, vol.9, 2017.
DOI : 10.3390/v9040084

URL : https://www.mdpi.com/1999-4915/9/4/84/pdf

W. H. Wilson, I. C. Gilg, A. Duarte, and H. Ogata, Development of DNA mismatch repair gene, MutS, as a diagnostic marker for detection and phylogenetic analysis of algal Megaviruses, Virology, pp.123-128, 2014.

C. Clerissi, N. Grimsley, L. Subirana, E. Maria, L. Oriol et al., Prasinovirus distribution in the Northwest Mediterranean Sea is affected by the environment and particularly by phosphate availability, Virology, pp.146-157, 2014.

S. Sunagawa, L. P. Coelho, S. Chaffron, J. R. Kultima, K. Labadie et al., Structure and function of the global ocean microbiome, Science, vol.348, p.1261359, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01233742

K. D. Yamada, K. Tomii, and K. Katoh, Application of the MAFFT sequence alignment program to large data-Reexamination of the usefulness of chained guide trees, Bioinformatics, vol.32, pp.3246-3251, 2016.

M. Suyama, D. Torrents, and P. Bork, PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments, Nucleic Acids Res, vol.34, pp.609-612, 2006.
DOI : 10.1093/nar/gkl315

URL : https://academic.oup.com/nar/article-pdf/34/suppl_2/W609/7623711/gkl315.pdf

S. R. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, pp.755-763, 1998.

L. Scola, B. Campocasso, A. Dong, R. Fournous, G. Barrassi et al., Tentative Characterization of new environmental giant viruses by MALDI-TOF mass spectrometry, Intervirology, vol.53, pp.344-353, 2010.

F. A. Matsen, R. B. Kodner, E. V. Armbrust, and . Pplacer, Linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree, BMC Bioinform, vol.11, 2010.
DOI : 10.1186/1471-2105-11-538

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-538

L. Fu, B. Niu, Z. Zhu, S. Wu, and W. Li, CD-HIT: Accelerated for clustering the next-generation sequencing data, Bioinformatics, vol.28, pp.3150-3152, 2012.
DOI : 10.1093/bioinformatics/bts565

URL : https://academic.oup.com/bioinformatics/article-pdf/28/23/3150/18529929/bts565.pdf

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat. Methods, vol.9, pp.357-359, 2012.
DOI : 10.1038/nmeth.1923

URL : http://europepmc.org/articles/pmc3322381?pdf=render

A. Untergasser, I. Cutcutache, T. Koressaar, J. Ye, B. C. Faircloth et al., Primer3-New capabilities and interfaces, Nucleic Acids Res, vol.40, 2012.
DOI : 10.1093/nar/gks596

URL : https://academic.oup.com/nar/article-pdf/40/15/e115/25343564/gks596.pdf

P. Rice, I. Longden, and A. Bleasby, EMBOSS: The European Molecular Biology Open Software Suite, Trends Genet, vol.16, pp.276-277, 2000.
DOI : 10.1016/s0168-9525(00)02024-2

S. Kimura, T. Yoshida, N. Hosoda, T. Honda, S. Kuno et al., Diurnal infection patterns and impact of Microcystis cyanophages in a Japanese pond, Appl. Environ. Microbiol, vol.78, pp.5805-5811, 2012.

, Metagenomic Sequencing Library Preparation, p.13, 2018.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet J, vol.17, pp.10-12, 2011.
DOI : 10.14806/ej.17.1.200

T. Mago? and S. L. Salzberg, FLASH: Fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, pp.2957-2963, 2011.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: A flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014.
DOI : 10.1093/bioinformatics/btu170

URL : https://academic.oup.com/bioinformatics/article-pdf/30/15/2114/17143152/btu170.pdf

R. C. Edgar, B. J. Haas, J. C. Clemente, C. Quince, and R. Knight, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.27, pp.2194-2200, 2011.
DOI : 10.1093/bioinformatics/btr381

URL : https://academic.oup.com/bioinformatics/article-pdf/27/16/2194/16901078/btr381.pdf

J. G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman et al., QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, vol.7, pp.335-336, 2010.
DOI : 10.1038/nmeth.f.303

URL : http://europepmc.org/articles/pmc3156573?pdf=render

P. J. Cock, T. Antao, J. T. Chang, B. A. Chapman, C. J. Cox et al., Freely available Python tools for computational molecular biology and bioinformatics, vol.25, pp.1422-1423, 2009.
DOI : 10.1093/bioinformatics/btp163

URL : https://academic.oup.com/bioinformatics/article-pdf/25/11/1422/944180/btp163.pdf

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J. Mol. Biol, vol.215, pp.403-410, 1990.
DOI : 10.1006/jmbi.1990.9999

J. D. Hunter, Matplotlib: A 2D Graphics Environment, Comput. Sci. Eng, vol.9, pp.90-95, 2007.
DOI : 10.1109/mcse.2007.55

J. Huerta-cepas, F. Serra, and P. Bork, ETE 3: Reconstruction, analysis, and visualization of phylogenomic data, Mol.Biol. Evol, vol.33, pp.1635-1638, 2016.
DOI : 10.1093/molbev/msw046

URL : https://academic.oup.com/mbe/article-pdf/33/6/1635/7953632/msw046.pdf

C. M. Deeg, C. T. Chow, and C. A. Suttle, The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea, vol.7, 2018.

F. Schulz, N. Yutin, N. N. Ivanova, D. R. Ortega, T. K. Lee et al., Giant viruses with an expanded complement of translation system components, vol.356, pp.82-85, 2017.
DOI : 10.1126/science.aal4657

URL : http://science.sciencemag.org/content/356/6333/82.full.pdf

A. Monier, J. B. Larsen, R. A. Sandaa, G. Bratbak, J. M. Claverie et al., Marine mimivirus relatives are probably large algal viruses, Virol. J, vol.5, 2008.
DOI : 10.1186/1743-422x-5-12

URL : https://virologyj.biomedcentral.com/track/pdf/10.1186/1743-422X-5-12

D. Vargas, C. Audic, S. Henry, N. Decelle, J. Mahé et al., Eukaryotic plankton diversity in the sunlit ocean, Science, vol.348, p.1261605, 2015.

C. Clerissi, N. Grimsley, H. Ogata, P. Hingamp, J. Poulain et al., Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine samples by using high-throughput sequencing analyses of PCR-amplified DNA polymerase and major capsid protein genes, Appl. Environ. Microbiol, vol.80, pp.3150-3160, 2014.

M. Moniruzzaman, E. R. Gann, G. R. Lecleir, Y. Kang, C. J. Gobler et al., Diversity and dynamics of algal Megaviridae members during a harmful brown tide caused by the pelagophyte, Aureococcus anophagefferens, FEMS Microbiol. Ecol, vol.92, 2016.

R. A. Sandaa, M. Heldal, T. Castberg, R. Thyrhaug, and G. Bratbak, Isolation and characterization of two viruses with large genome size infecting Chrysochromulina ericina (Prymnesiophyceae) and Pyramimonas orientalis (Prasinophyceae), Virology, vol.290, pp.272-280, 2001.
DOI : 10.1006/viro.2001.1161

URL : https://doi.org/10.1006/viro.2001.1161