Evolutionary ecology of virus emergence, Ann. N. Y. Acad. Sci, vol.1389, pp.124-146, 2017. ,
DOI : 10.1111/nyas.13304
The evolutionary genetics of viral emergence, Curr. Top. Microbiol. Immunol, vol.315, pp.51-66, 2007. ,
Recombination as a motor of host switches and virus emergence: Geminiviruses as case studies, Curr. Opin. Virol, vol.10, pp.14-19, 2015. ,
Why do RNA viruses recombine?, Nat. Rev. Microbiol, vol.9, pp.617-626, 2011. ,
DOI : 10.1038/nrmicro2614
URL : http://europepmc.org/articles/pmc3324781?pdf=render
Origins and evolution of viruses of eukaryotes: The ultimate modularity, Virology, pp.479-480, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977389
Multiple origins of viral capsid proteins from cellular ancestors, Proc. Natl. Acad. Sci, vol.114, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977364
The double-stranded DNA virosphere as a modular hierarchical network of gene sharing, vol.7, pp.978-994, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977375
Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses, Curr. Opin. Virol, vol.3, pp.578-586, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977403
A field guide to eukaryotic circular single-stranded DNA viruses: Insights gained from metagenomics, Arch. Virol, vol.157, pp.1851-1871, 2012. ,
Ton-Hoang, B. Breaking and joining single-stranded DNA: The HUH endonuclease superfamily, Nat. Rev. Microbiol, vol.11, pp.525-538, 2013. ,
A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses, FEBS Lett, vol.262, pp.145-148, 1990. ,
Evolutionary history of ssDNA bacilladnaviruses features horizontal acquisition of the capsid gene from ssRNA nodaviruses, Virology, vol.504, pp.114-121, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977365
Exploring the viral world through metagenomics, Curr. Opin. Virol, vol.1, pp.289-297, 2011. ,
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
Validation of high rates of nucleotide substitution in geminiviruses: Phylogenetic evidence from East African cassava mosaic viruses, J. Gen. Virol, vol.90, issue.6, pp.1539-1547, 2009. ,
Insights into the evolutionary history of an emerging livestock pathogen: Porcine circovirus 2, J. Virol, vol.83, pp.12813-12821, 2009. ,
High variability and rapid evolution of a nanovirus, J. Virol, vol.84, pp.9105-9117, 2010. ,
Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts, Virol. J, vol.6, 2009. ,
Widely conserved recombination patterns among single-stranded DNA viruses, J. Virol, vol.83, pp.2697-2707, 2009. ,
Recombination in eukaryotic single stranded DNA viruses, Viruses, vol.3, pp.1699-1738, 2011. ,
URL : https://hal.archives-ouvertes.fr/halshs-00637518
Possible emergence of new geminiviruses by frequent recombination, Virology, vol.265, pp.218-225, 1999. ,
Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses, Sci. Rep, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977398
Deep recombination: RNA and ssDNA virus genes in DNA virus and host genomes, Annu. Rev. Virol, vol.2, pp.203-217, 2015. ,
A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses, Biol. Direct, vol.7, p.13, 2012. ,
Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses, Nat. Commun, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00881062
Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing, Genome Biol. Evol, vol.7, pp.993-1001, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977388
Diversity and comparative genomics of chimeric viruses in Sphagnum-dominated peatlands, Virus Evol, vol.2, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977372
Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae, Virus Evol, vol.3, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977359
Smacoviridae: A new family of animal-associated single-stranded DNA viruses, Arch. Virol, 2018. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977338
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability, Mol. Biol. Evol, vol.30, pp.772-780, 2013. ,
trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009. ,
Smart Model Selection in PhyML, Mol. Biol. Evol, vol.34, pp.2422-2424, 2017. ,
URL : https://hal.archives-ouvertes.fr/lirmm-01794206
RDP4: Detection and analysis of recombination patterns in virus genomes, Virus Evol, vol.1, 2015. ,
Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks, Syst. Biol, vol.61, pp.1061-1067, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-02154987
A sequence logo generator, Genome Res, vol.14, pp.1188-1190, 2004. ,
Capulavirus and Grablovirus: Two new genera in the family Geminiviridae, Arch. Virol, vol.162, pp.1819-1831, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01607449
Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks, PLoS Pathog, 2011. ,
Extensive recombination-induced disruption of genetic interactions is highly deleterious but can be partially reversed by small numbers of secondary recombination events, J. Virol, vol.88, pp.7843-7851, 2014. ,
Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses, J. Virol, vol.88, 1972. ,
Alphasatellitidae: A new family with two subfamilies for the classification of geminivirus-and nanovirus-associated alphasatellites, Arch. Virol, 2018. ,
Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan. Front. Microbiol, vol.9, 2018. ,
Diverse small circular DNA viruses circulating amongst estuarine molluscs, Infect. Genet. Evol, vol.31, pp.284-295, 2015. ,
Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces, Arch. Virol, vol.160, pp.353-358, 2015. ,
A diverse group of small circular ssDNA viral genomes in human and non-human primate stools ,
The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin, Arch. Virol, vol.161, pp.959-966, 2016. ,
Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes, Virol. J, vol.15, 2018. ,
Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta), J. Gen. Virol, vol.12, pp.2668-2681, 1993. ,
Diverse circovirus-like genome architectures revealed by environmental metagenomics, J. Gen. Virol, vol.10, pp.2418-2424, 2009. ,
Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins, Front. Microbiol, vol.6, 2015. ,
Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem, Infect. Genet. Evol, vol.39, pp.304-316, 2016. ,
Novel circular DNA viruses in stool samples of wild-living chimpanzees, J. Gen. Virol, p.91, 2010. ,
A new family of widespread single-stranded DNA viruses, Arch. Virol, vol.161, pp.2633-2643, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977377
, This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license, © 2018 by the authors. Licensee MDPI