Y. Z. Zhang, Y. M. Chen, W. Wang, X. C. Qin, and E. C. Holmes, Expanding the RNA virosphere by unbiased metagenomics, Annu. Rev. Virol, vol.6, pp.119-139, 2019.

V. V. Dolja and E. V. Koonin, Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer, Virus Res, vol.244, pp.36-52, 2018.

P. Lefeuvre, Evolution and ecology of plant viruses, Nat. Rev. Microbiol, vol.17, pp.632-644, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02627595

D. J. Obbard, Expansion of the metazoan virosphere: progress, pitfalls, and prospects, Curr. Opin. Virol, vol.31, pp.17-23, 2018.

J. R. Brum and M. B. Sullivan, Rising to the challenge: accelerated pace of discovery transforms marine virology, Nat. Rev. Microbiol, vol.13, pp.147-159, 2015.

D. Backstrom, Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism, vol.10, pp.2497-2515, 2019.

L. Zhao, K. Rosario, M. Breitbart, and S. Duffy, Eukaryotic circular rep-encoding single-stranded DNA (CRESS DNA) viruses: ubiquitous viruses with small genomes and a diverse host range, Adv. Virus Res, vol.103, pp.71-133, 2019.

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

A. C. Gregory, Marine DNA viral macro-and microdiversity from pole to pole, Cell, vol.177, pp.1109-1123, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02387010

P. Simmonds, Consensus statement: virus taxonomy in the age of metagenomics, Nat. Rev. Microbiol, vol.15, pp.161-168, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01977366

M. Vlok, A. S. Lang, and C. A. Suttle, Marine RNA virus quasispecies are distributed throughout the oceans, vol.4, pp.157-176, 2019.

A. L. Greninger, A decade of RNA virus metagenomics is (not) enough, Virus Res, vol.244, pp.218-229, 2018.

A. B. Janowski, Statoviruses, a novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals, Virology, vol.504, pp.36-44, 2017.

J. A. Miranda, A. I. Culley, C. R. Schvarcz, and G. F. Steward, RNA viruses as major contributors to Antarctic virioplankton, Environ. Microbiol, vol.18, pp.3714-3727, 2016.

T. F. Ng, High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage, J. Virol, vol.86, pp.12161-12175, 2012.

F. M. Waldron, G. N. Stone, and D. J. Obbard, Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes, PLoS Genet, vol.14, p.1007533, 2018.

M. Shi, The evolutionary history of vertebrate RNA viruses, Nature, vol.556, pp.197-202, 2018.

A. Lopez-bueno, A. Rastrojo, R. Peiro, M. Arenas, and A. Alcami, Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake, Mol. Ecol, vol.24, pp.4812-4825, 2015.

M. Moniruzzaman, Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics, Nat. Commun, vol.8, p.16054, 2017.

K. Rosario, C. Nilsson, Y. W. Lim, Y. Ruan, and M. Breitbart, Metagenomic analysis of viruses in reclaimed water, Environ. Microbiol, vol.11, pp.2806-2820, 2009.

A. S. Lang, A. I. Culley, and C. A. Suttle, Genome sequence and characterization of a virus (HaRNAV) related to picorna-like viruses that infects the marine toxic bloom-forming alga Heterosigma akashiwo, Virology, vol.320, pp.206-217, 2004.

K. Nagasaki, Dinoflagellates, diatoms, and their viruses, J. Microbiol, vol.46, pp.235-243, 2008.

Y. Shirai, Isolation and characterization of a single-stranded RNA virus infecting the marine planktonic diatom Chaetoceros tenuissimus Meunier, Appl. Environ. Microbiol, vol.74, pp.4022-4027, 2008.

Y. Tomaru, Y. Takao, H. Suzuki, T. Nagumo, and K. Nagasaki, Isolation and characterization of a single-stranded RNA virus infecting the bloom-forming diatom Chaetoceros socialis, Appl. Environ. Microbiol, vol.75, pp.2375-2381, 2009.

K. Kimura and Y. Tomaru, Discovery of two novel viruses expands the diversity of single-stranded DNA and single-stranded RNA viruses infecting a cosmopolitan marine diatom, Appl. Environ. Microbiol, vol.81, pp.1120-1131, 2015.

Y. Takao, K. Mise, K. Nagasaki, T. Okuno, and D. Honda, Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp, J. Gen. Virol, vol.87, pp.723-733, 2006.

J. A. Gustavsen, D. M. Winget, X. Tian, and C. A. Suttle, High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities, Front. Microbiol, vol.5, p.703, 2014.

M. Vlok, A. S. Lang, and C. A. Suttle, Application of a sequence-based taxonomic classification method to uncultured and unclassified marine single-stranded RNA viruses in the order Picornavirales, Virus Evol, vol.5, p.56, 2019.

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, Redefining the invertebrate RNA virosphere, Nature, vol.540, pp.539-543, 2016.

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, 2016.

J. R. Fauver, West African Anopheles gambiae mosquitoes harbor a taxonomically diverse virome including new insect-specific flaviviruses, mononegaviruses, and totiviruses, Virology, vol.498, pp.288-299, 2016.

C. L. Webster, The discovery, distribution, and evolution of viruses associated with Drosophila melanogaster, PLoS Biol, vol.13, p.1002210, 2015.

D. Grybchuk, Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania, Proc. Natl Acad. Sci. USA, vol.115, pp.506-515, 2018.

S. Y. Marzano, Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens, J. Virol, vol.90, pp.6846-6863, 2016.

I. Kotta-loizou and R. H. Coutts, Studies on the virome of the entomopathogenic fungus Beauveria bassiana reveal novel dsRNA elements and mild hypervirulence, PLoS Pathog, vol.13, p.1006183, 2017.

S. R. Krishnamurthy, A. B. Janowski, G. Zhao, D. Barouch, and D. Wang, Hyperexpansion of RNA bacteriophage diversity, PLoS Biol, vol.14, p.1002409, 2016.

M. J. Roossinck, Evolutionary and ecological links between plant and fungal viruses, N. Phytol, vol.221, pp.86-92, 2018.

A. Culley, New insight into the RNA aquatic virosphere via viromics, Virus Res, vol.244, pp.84-89, 2018.

S. R. Coy, E. R. Gann, H. L. Pound, S. M. Short, and S. W. Wilhelm, Viruses of eukaryotic algae: diversity, methods for detection, and future directions, Viruses, vol.10, p.487, 2018.

J. Callanan, Expansion of known ssRNA phage genomes: from tens to over a thousand, Sci. Adv, vol.6, p.5981, 2020.

Y. I. Wolf, Origins and evolution of the global RNA virome, vol.9, pp.2329-2347, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01977324

J. H. Kuhn, Classify viruses-the gain is worth the pain, Nature, vol.566, pp.318-320, 2019.
URL : https://hal.archives-ouvertes.fr/pasteur-02043332

E. V. Koonin, Global organization and proposed megataxonomy of the virus world. Micobiol, Mol. Biol. Rev, vol.84, pp.61-80, 2020.
URL : https://hal.archives-ouvertes.fr/pasteur-02558270

C. F. Kranzler, Silicon limitation facilitates virus infection and mortality of marine diatoms, Nat. Microbiol, vol.4, pp.1790-1797, 2019.

S. M. Valles, ICTV virus taxonomy profile: Dicistroviridae, J. Gen. Virol, vol.98, pp.355-356, 2017.

F. Revers and J. A. Garcia, Molecular biology of Potyviruses, Adv. Virus Res, vol.92, pp.101-199, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02801855

A. J. Gibbs, M. Hajizadeh, K. Ohshima, and R. A. Jones, The Potyviruses: an evolutionary synthesis is emerging, Viruses, vol.12, p.132, 2020.

V. V. Dolja, M. Krupovic, and E. V. Koonin, Deep roots and splendid boughs of the global plant virome, Annu. Rev. Phytopathol, vol.58, 2020.
URL : https://hal.archives-ouvertes.fr/pasteur-02861246

E. V. Koonin, V. V. Dolja, and M. Krupovic, Origins and evolution of viruses of eukaryotes: the ultimate modularity, Virology, vol.479, p.25, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977389

V. V. Dolja, V. P. Boyko, A. A. Agranovsky, and E. V. Koonin, Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation, Virology, vol.184, pp.79-86, 1991.

X. Agirrezabala, The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses, vol.4, p.11795, 2015.

M. Zamora, Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses, Sci. Adv, vol.3, p.2182, 2017.

V. V. Dolja and E. V. Koonin, Common origins and host-dependent diversity of plant and animal viromes, Curr. Opin. Virol, vol.1, pp.322-331, 2011.

M. A. Felix, Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses, PLoS Biol, vol.9, p.1000586, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00566941

T. Yokoi, S. Yamashita, and T. Hibi, The nucleotide sequence and genome organization of Sclerophthora macrospora virus A, Virology, vol.311, pp.394-399, 2003.

M. Heller-dohmen, J. C. Gopfert, J. Pfannstiel, and O. Spring, The nucleotide sequence and genome organization of Plasmopara halstedii virus, Virol. J, vol.8, p.123, 2011.

B. Scholz, Zoosporic parasites infecting marine diatoms-a black box that needs to be opened, Fungal Ecol, vol.19, pp.59-76, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01253978

B. H. Meldal, An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa, Mol. Phylogenet. Evol, vol.42, pp.622-636, 2007.

B. Bolduc, Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs, J. Virol, vol.86, pp.5562-5573, 2012.

D. S. Ferrero, M. Buxaderas, J. F. Rodriguez, and N. Verdaguer, The structure of the RNA-dependent RNA polymerase of a permutotetravirus suggests a link between primer-dependent and primer-independent polymerases, PLoS Pathog, vol.11, p.1005265, 2015.

A. E. Gorbalenya, The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage, J. Mol. Biol, vol.324, pp.47-62, 2002.

S. Sabanadzovic, N. A. Ghanem-sabanadzovic, and A. E. Gorbalenya, Permutation of the active site of putative RNA-dependent RNA polymerase in a newly identified species of plant alpha-like virus, Virology, vol.394, pp.1-7, 2009.

A. L. Greninger and J. L. Derisi, Draft genome sequences of ciliovirus and brinovirus from San Francisco wastewater, Genome Announc, vol.3, pp.651-666, 2015.

B. I. Hillman and G. Cai, The family Narnaviridae: simplest of RNA viruses, Adv. Virus Res, vol.86, pp.149-176, 2013.

F. Schmidt, M. Y. Cherepkova, and R. J. Platt, Transcriptional recording by CRISPR spacer acquisition from RNA, Nature, vol.562, pp.380-385, 2018.

C. Lauber, M. Seifert, R. Bartenschlager, and S. Seitz, Discovery of highly divergent lineages of plant-associated astro-like viruses sheds light on the emergence of potyviruses, Virus Res, vol.260, pp.38-48, 2019.

G. Sun, Efficient purification and concentration of viruses from a large body of high turbidity seawater, vol.1, pp.197-206, 2014.

M. R. Henn, Analysis of high-throughput sequencing and annotation strategies for phage genomes, PLoS ONE, vol.5, p.9083, 2010.

M. Steinegger and J. Soding, MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets, Nat. Biotechnol, vol.35, pp.1026-1028, 2017.

R. C. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinform, vol.5, p.113, 2004.

J. Soding, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, pp.951-960, 2005.

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

A. Marchler-bauer, CDD: NCBI's conserved domain database, Nucleic Acids Res, vol.43, pp.222-226, 2015.

N. Yutin, Y. I. Wolf, D. Raoult, and E. V. Koonin, Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution, Virol. J, vol.6, p.223, 2009.

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

N. Yutin, Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut, Nat. Microbiol, vol.3, pp.38-46, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01977350

M. Mirdita, Uniclust databases of clustered and deeply annotated protein sequences and alignments, Nucleic Acids Res, vol.45, pp.170-176, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02088268

M. Remmert, A. Biegert, A. Hauser, and J. Soding, HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment, Nat. Methods, vol.9, pp.173-175, 2011.

T. Frickey and A. Lupas, CLANS: a Java application for visualizing protein families based on pairwise similarity, Bioinformatics, vol.20, pp.3702-3704, 2004.

A. L. Mitchell, EBI metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies, Nucleic Acids Res, vol.46, pp.726-735, 2018.

S. R. Eddy, Accelerated profile HMM searches, PLoS Comput. Biol, vol.7, p.1002195, 2011.

S. A. Shmakov, The CRISPR spacer space is dominated by sequences from species-specific mobilomes, vol.8, pp.1397-1414, 2017.

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

, Extended Data Fig. 4 | A nucleotide sequence match between a Yangshan RNA virome contig bearing a levi-like RdRP (bottom line) and the type III-B CRISPR spacer locus of the bacterium Candidatus Accumulibacter sp