F. C. Ballaud, Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat, Frontiers in Microbiology, vol.6, p.1494, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01263117

P. Bernardo, Identification and Characterisation of a Highly Divergent Geminivirus: Evolutionary and Taxonomic Implications, Virus Research, vol.177, pp.35-45, 2013.

J. Colombet, Virioplankton 'Pegylation': Use of PEG (Polyethylene Glycol) to Concentrate and Purify Viruses in Pelagic Ecosystems, Journal of Microbiological Methods, vol.71, pp.212-221, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00525979

A. Dayaram, Diverse Circular Replication-Associated Protein Encoding Viruses Circulating in Invertebrates Within a Lake Ecosystem, Infection, Genetics and Evolution, vol.39, pp.304-320, 2016.

G. S. Diemer and K. M. Stedman, A Novel Virus Genome Discovered in an Extreme Environment Suggests Recombination Between Unrelated Groups of RNA and DNA Viruses, Biology Direct, vol.7, p.13, 2012.

R. C. Edgar, MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput, Nucleic Acids Research, vol.32, pp.1792-1799, 2004.

J. A. Fuhrman, Marine Viruses and Their Biogeochemical and Ecological Effects, Nature, vol.399, pp.541-549, 1999.

S. Guindon, New Alogrithms and Methods to Estimate Maximum-Likelihoods Phylogenies: Assessing the Performance of PhyML 3.0', Systematic Biology, vol.59, pp.307-328, 2010.

I. Hewson, Metagenomic Identification, Seasonal Dynamics, and Potential Transmission Mechanisms of a Daphnia-Associated Single-Stranded DNA Virus in Two Temperate Lakes, Limnology and Oceanography, vol.58, pp.1605-1625, 2013.

G. Jobb, A. Von-haeseler, and K. Strimmer, TREEFINDER: a Powerful Graphical Analysis Environment for Molecular Phylogenetics, BMC Evolutionary Biology, vol.4, p.18, 2004.

K. Kim and J. Bae, Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded And Double-Stranded DNA Viruses, Applied and Environmental Microbiology, vol.77, pp.7663-7671, 2011.

S. Kraberger, Characterisation of a Diverse Range of Circular Replication-Associated Protein Encoding DNA Viruses Recovered From a Sewage Treatment Oxidation Pond, Infection, Genetics and Evolution, vol.31, pp.73-86, 2015.

M. Krupovic and P. Forterre, Single-Stranded DNA Viruses Employ a Variety of Mechanisms for Integration into Host Genomes, Annals of the New York Academy of Sciences, vol.3, p.2633, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01436107

S. Kurtz, Versatile and Open Software for Comparing Large Genomes, Genome Biology, vol.5, p.12, 2004.

L. Bras and Y. , Towards a Life Sciences Virtual Research Environment, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01102438

W. Ludwig, ARB: A Software Environment for Sequence Data, Nucleic Acids Research, vol.32, pp.1363-71, 2004.

M. F. Male, Cycloviruses, Gemycircularviruses and Other Novel Replication-Associated Protein Encoding Circular Viruses in Pacific Flying Fox (Pteropus tonganus) Faeces', Infection, Genetics and Evolution, vol.39, pp.279-92, 2016.

L. D. Mcdaniel, Comparative Metagenomics: Natural Populations of Induced Prophages Demonstrate Highly Unique, Lower Diversity Viral Sequences, Environmental Microbiology, vol.16, pp.570-85, 2014.

B. M. Muhire, A. Varsani, M. , and D. P. , SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation, PLoS One, vol.9, p.108277, 2014.

J. Pei, B. H. Kim, and N. V. Grishin, PROMALS3D: A Tool for Multiple Protein Sequence and Structure Alignments, Nucleic Acids Research, vol.36, pp.2295-300, 2008.

E. F. Pettersen, UCSF Chimera-a Visualization System for Exploratory Research and Analysis, Journal of Computational Chemistry, vol.25, pp.1605-1617, 2004.

A. Quaiser, Diversity and Comparative Genomics of Microviridae in Sphagnum-Dominated Peatlands, Frontiers in Microbiology, vol.6, p.375, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01149546

K. Rosario, S. Duffy, and M. Breitbart, A Field Guide to Eukaryotic Circular Single-Stranded DNA Viruses: Insights Gained From Metagenomics, Archives of Virology, vol.157, pp.1851-71, 2012.

S. Roux, Chimeric Viruses Blur the Borders Between the Major Groups of Eukaryotic Single-Stranded DNA Viruses, Nature Communications, vol.4, p.2700, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00881062

K. M. Stedman, Deep Recombination: RNA and ssDNA Virus Genes in DNA Virus and Host Genomes, Annual Review of Virology, vol.2, pp.203-220, 2015.

O. Steel, Circular Replication-Associated Protein Encoding DNA Viruses Identified in the Faecal Matter of Various Animals in New Zealand', Infection, Genetics and Evolution, vol.43, pp.151-64, 2016.

C. A. Suttle, Marine Viruses-Major Players in the Global Ecosystem, Nature Reviews Microbiology, vol.5, pp.801-813, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01663342

K. E. Wommack and R. R. Colwell, Virioplankton: Viruses in Aquatic Ecosystems, Microbiology and Molecular Biology Reviews, vol.64, pp.69-114, 2000.

E. A. Wright, Splicing Features in Maize Streak Virus Virion-and Complementary-Sense Gene Expression, The Plant Journal, vol.12, pp.1285-97, 1997.