R. A. Edwards and F. Rohwer, Viral metagenomics, Nat. Rev. Microbiol, vol.3, pp.504-510, 2005.

J. L. Mokili, F. Rohwer, and B. E. Dutilh, Metagenomics and future perspectives in virus discovery, Curr. Opin. Virol, vol.2, pp.63-77, 2012.

K. Rosario and M. Breitbart, Exploring the viral world through metagenomics, Curr. Opin. Virol, vol.1, pp.289-297, 2011.

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

C. H. Wigington, Re-e xamination of the relationship between marine virus and microbial cell abundances, Nat. Microbiol, vol.1, p.15024, 2016.

C. A. Suttle, Viruses: unlocking the greatest biodiversity on Earth, Genome, vol.56, pp.542-544, 2013.

M. J. Roossinck, Move over, bacteria! Viruses make their mark as mutualistic microbial symbionts, J. Virol, vol.89, pp.6532-6535, 2015.

G. F. Steward, Are we missing half of the viruses in the ocean?, ISME J, vol.7, pp.672-679, 2013.

P. Simmonds, Methods for virus classification and the challenge of incorporating metagenomic sequence data, J. Gen. Virol, vol.96, pp.1193-1206, 2015.

M. Krupovic, S. A. Ghabrial, D. Jiang, and A. Varsani, Genomoviridae: a new family of widespread singlestranded DNA viruses, Arch. Virol, vol.161, pp.2633-2643, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977377

J. M. Labonte and C. A. Suttle, Previously unknown and highly divergent ssDNA viruses populate the oceans, ISME J, vol.7, pp.2169-2177, 2013.

A. Dayaram, Diverse small circular DNA viruses circulating amongst estuarine molluscs, Infect. Genet. Evol, vol.31, pp.284-295, 2015.

A. Dayaram, Diverse circular replicationassociated protein encoding viruses circulating in invertebrates within a lake ecosystem, Infect. Genet. Evol, vol.39, pp.304-316, 2016.

K. Rosario, R. O. Schenck, R. C. Harbeitner, S. N. Lawler, and M. Breitbart, Novel circular singlestranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins, Front. Microbiol, vol.6, p.696, 2015.

N. Yutin, S. Shevchenko, V. Kapitonov, M. Krupovic, and E. V. Koonin, A novel group of diverse Polinton-like viruses discovered by metagenome analysis, BMC Biol, vol.13, p.95, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977381

J. Zhou, Diversity of virophages in metagenomic data sets, J. Virol, vol.87, pp.4225-4236, 2013.

B. E. Dutilh, A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes, Nat. Commun, vol.5, p.4498, 2014.

N. Yutin, V. V. Kapitonov, and E. V. Koonin, A new family of hybrid virophages from an animal gut metagenome, Biol. Direct, vol.10, p.19, 2015.

W. Zhang, Four novel algal virus genomes discovered from Yellowstone Lake metagenomes, Sci. Rep, vol.5, p.15131, 2015.

S. Yau, Virophage control of antarctic algal host-virus dynamics, Proc. Natl Acad. Sci. USA, vol.108, pp.6163-6168, 2011.

J. R. Brum, Ocean plankton. Patterns and ecological drivers of ocean viral communities, Science, vol.348, p.1261498, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01275276

F. E. Angly, The marine viromes of four oceanic regions, PLoS Biol, vol.4, p.368, 2006.

M. Breitbart, Diversity and population structure of a near-shore marine-sediment viral community, Proc. Biol. Sci, vol.271, pp.565-574, 2004.

D. Paez-espino, Uncovering Earth's virome, Nature, vol.536, pp.425-430, 2016.

A. I. Culley, The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics, vol.5, pp.1210-1224, 2014.

S. Kraberger, Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond, Infect. Genet. Evol, vol.31, pp.73-86, 2015.

M. J. Roossinck, Plants, viruses and the environment: ecology and mutualism. Virology 479-480, pp.271-277, 2015.

J. M. Labonte, S. J. Hallam, and C. A. Suttle, Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment, Front. Microbiol, vol.6, p.315, 2015.

A. J. Szekely and M. Breitbart, Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology, FEMS Microbiol. Lett, vol.363, p.27, 2016.

M. Hopkins, Diversity of environmental singlestranded DNA phages revealed by PCR amplification of the partial major capsid protein, ISME J, vol.8, pp.2093-2103, 2014.

S. Roux, M. Krupovic, A. Poulet, D. Debroas, and F. Enault, Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads, PLoS ONE, vol.7, p.40418, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00816089

K. Rosario, S. Duffy, and M. Breitbart, A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics, Arch. Virol, vol.157, pp.1851-1871, 2012.

M. J. Roossinck, Plant virus metagenomics: biodiversity and ecology, Annu. Rev. Genet, vol.46, pp.359-369, 2012.

C. X. Li, Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses, vol.4, p.5378, 2015.

M. Shi, Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses, J. Virol, vol.90, pp.659-669, 2015.

O. Zablocki, High-level diversity of tailed phages, eukaryote-associated viruses, and virophage-like elements in the metaviromes of antarctic soils, Appl. Environ. Microbiol, vol.80, pp.6888-6897, 2014.

S. Roux, S. J. Hallam, T. Woyke, and M. B. Sullivan, Viral dark matter and virus-host interactions resolved from publicly available microbial genomes, vol.4, p.8490, 2015.

B. Bolduc, K. Youens-clark, S. Roux, B. L. Hurwitz, and M. B. Sullivan, iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure, 2016.

E. V. Koonin, T. G. Senkevich, and V. V. Dolja, The ancient Virus World and evolution of cells, Biol. Direct, vol.1, p.29, 2006.

E. C. Holmes, What does virus evolution tell us about virus origins?, J. Virol, vol.85, pp.5247-5251, 2011.

E. V. Koonin and V. V. Dolja, A virocentric perspective on the evolution of life, Curr. Opin. Virol, vol.3, pp.546-557, 2013.

F. Rohwer and R. Edwards, The Phage Proteomic Tree: a genome-based taxonomy for phage, J. Bacteriol, vol.184, pp.4529-4535, 2002.

C. R. Woese, Bacterial evolution, Microbiol. Rev, vol.51, pp.221-271, 1987.

M. A. O'malley and E. V. Koonin, How stands the Tree of Life a century and a half after The Origin?, Biol. Direct, vol.6, p.32, 2011.

N. R. Pace, J. Sapp, and N. Goldenfeld, Phylogeny and beyond: scientific, historical, and conceptual significance of the first tree of life, Proc. Natl Acad. Sci. USA, vol.109, pp.1011-1018, 2012.

M. J. Adams, Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses, Arch. Virol, vol.161, pp.2921-2949, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977376

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

P. Colson, 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

M. H. Van-regenmortel, Classes, taxa and categories in hierarchical virus classification: a review of current debates on definitions and names of virus species, Bionomina, vol.10, pp.1-21, 2016.

Y. Cai, Nonhuman transferrin receptor 1 is an efficient cell entry receptor for Ocozocoautla de Espinosa virus, J. Virol, vol.87, pp.13930-13935, 2013.

A. Kapoor, P. Simmonds, W. I. Lipkin, S. Zaidi, and E. Delwart, Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses, J. Virol, vol.84, pp.10322-10328, 2010.

Q. L. Choo, Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome, Science, vol.244, pp.359-362, 1989.

G. Kuo, An assay for circulating antibodies to a major etiologic virus of human non-A, non-B hepatitis, Science, vol.244, pp.362-364, 1989.

A. Acevedo and R. Andino, Library preparation for highly accurate population sequencing of RNA viruses, Nat. Protoc, vol.9, pp.1760-1769, 2014.

B. L. Hurwitz and M. B. Sullivan, The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology, PLoS ONE, vol.8, p.57355, 2013.

G. Lima-mendez, J. Van-helden, A. Toussaint, and R. Leplae, Reticulate representation of evolutionary and functional relationships between phage genomes, Mol. Biol. Evol, vol.25, pp.762-777, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01624306

C. Lauber and A. E. Gorbalenya, Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses, J. Virol, vol.86, pp.3890-3904, 2012.

G. F. Hatfull and R. W. Hendrix, Bacteriophages and their genomes, Curr. Opin. Virol, vol.1, pp.298-303, 2011.

E. V. Koonin, Y. I. Wolf, K. Nagasaki, and V. V. Dolja, The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups, Nat. Rev. Microbiol, vol.6, pp.925-939, 2008.

L. Li, Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces, J. Virol, vol.84, pp.1674-1682, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01375296

O. Steel, Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand, Infect. Genet. Evol, vol.43, pp.151-164, 2016.

C. T. Parker, B. J. Tindall, and G. M. Garrity, International Code of Nomenclature of Prokaryotes, Int. J. Syst. Evol. Microbiol, 2015.

K. T. Konstantinidis and R. Rossello-mora, Classifying the uncultivated microbial majority: a place for metagenomic data in the Candidatus proposal, Syst. Appl. Microbiol, vol.38, pp.223-230, 2015.

B. P. Hedlund, J. A. Dodsworth, and J. T. Staley, The changing landscape of microbial biodiversity exploration and its implications for systematics, Syst. Appl. Microbiol, vol.38, pp.231-236, 2015.

R. G. Murray and E. Stackebrandt, Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes, Int. J. Syst. Bacteriol, vol.45, pp.186-187, 1995.

D. L. Hawksworth, The Amsterdam declaration on fungal nomenclature, IMA Fungus, vol.2, pp.105-112, 2011.

C. L. Schoch, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi, Proc. Natl Acad. Sci. USA, vol.109, pp.6241-6246, 2012.

D. S. Hibbett and J. W. Taylor, Fungal systematics: is a new age of enlightenment at hand?, Nat. Rev. Microbiol, vol.11, pp.129-133, 2013.

S. Roux, 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

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, pp.3059-3066, 2002.

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2approximately maximum-likelihood trees for large alignments, PLoS ONE, vol.5, p.9490, 2010.