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Viruses 2018, 10(4), 187; https://doi.org/10.3390/v10040187

Pervasive Chimerism in the Replication-Associated Proteins of Uncultured Single-Stranded DNA Viruses

1
Institute of Biotechnology, Vilnius University, Saulėtekio Av. 7, Vilnius 10257, Lithuania
2
Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
3
The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
4
Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory 7700, South Africa
*
Author to whom correspondence should be addressed.
Received: 23 March 2018 / Revised: 4 April 2018 / Accepted: 8 April 2018 / Published: 10 April 2018
(This article belongs to the Special Issue Viral Recombination: Ecology, Evolution and Pathogenesis)
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Abstract

Numerous metagenomic studies have uncovered a remarkable diversity of circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses, the majority of which are uncultured and unclassified. Unlike capsid proteins, the Reps show significant similarity across different groups of CRESS DNA viruses and have conserved domain organization with the N-terminal nuclease and the C-terminal helicase domain. Consequently, Rep is widely used as a marker for identification, classification and assessment of the diversity of CRESS DNA viruses. However, it has been shown that in certain viruses the Rep nuclease and helicase domains display incongruent evolutionary histories. Here, we systematically evaluated the co-evolutionary patterns of the two Rep domains across classified and unclassified CRESS DNA viruses. Our analysis indicates that the Reps encoded by members of the families Bacilladnaviridae, Circoviridae, Geminiviridae, Genomoviridae, Nanoviridae and Smacoviridae display largely congruent evolutionary patterns in the two domains. By contrast, among the unclassified CRESS DNA viruses, 71% appear to have chimeric Reps. Such massive chimerism suggests that unclassified CRESS DNA viruses represent a dynamic population in which exchange of gene fragments encoding the nuclease and helicase domains is extremely common. Furthermore, purging of the chimeric sequences uncovered six monophyletic Rep groups that may represent new families of CRESS DNA viruses. View Full-Text
Keywords: CRESS DNA viruses; virus evolution; rolling-circle replication initiation proteins; ssDNA viruses; superfamily 3 helicase domain; HUH endonuclease domain; recombination CRESS DNA viruses; virus evolution; rolling-circle replication initiation proteins; ssDNA viruses; superfamily 3 helicase domain; HUH endonuclease domain; recombination
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Kazlauskas, D.; Varsani, A.; Krupovic, M. Pervasive Chimerism in the Replication-Associated Proteins of Uncultured Single-Stranded DNA Viruses. Viruses 2018, 10, 187.

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