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The evolution, distribution and diversity and of endogenous circoviral elements

Tristan P.W Dennis, William Marciel de Souza, Soledad Marsile-Medun, Joshua B. Singer, Sam J. Wilson, Robert J. Gifford
doi: https://doi.org/10.1101/207399
Tristan P.W Dennis
1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK
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William Marciel de Souza
1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK
2Virology Research Center, School of Medicine of Ribeirão Preto of University of São Paulo, Ribeirão Preto, Brazil
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Soledad Marsile-Medun
1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK
3Agrocampus Ouest, 65 Rue de Saint-Brieuc, 35000 Rennes, France
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Joshua B. Singer
1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK
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Sam J. Wilson
1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK
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Robert J. Gifford
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Abstract

Circoviruses (family Circoviridae) are small, non-enveloped viruses that have short, single-stranded DNA genomes. Circovirus sequences are frequently recovered in metagenomic investigations, indicating that these viruses are widespread, yet they remain relatively poorly understood. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in vertebrate genomes. CVe can provide unique, retrospective information about the biology and evolution of circoviruses. In this study, we screened 362 vertebrate genome assemblies in silico to generate a catalog of CVe loci. We identified a total of 179 CVe sequences, most of which have not been reported previously. We show that these CVe loci reflect at least 19 distinct germline integration events. We determine the structure of CVe loci, identifying some that show evidence of potential functionalization. We also identify orthologous copies of CVe in snakes, fish, birds, and mammals, allowing us to add new calibrations to the timeline of circovirus evolution. Finally, we observed that some ancient CVe group robustly with contemporary circoviruses in phylogenies, with all sequences within these groups being derived from the same host class or order, implying a hitherto underappreciated stability in circovirus-host relationships. The openly available dataset constructed in this investigation provides new insights into circovirus evolution, and can be used to facilitate further studies of circoviruses and CVe.

CVe
endogenous circoviral element
ORF
open reading frame
Cap
Capsid
Rep
Replicase
ssDNA
single-stranded DNA
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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 16, 2018.
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The evolution, distribution and diversity and of endogenous circoviral elements
Tristan P.W Dennis, William Marciel de Souza, Soledad Marsile-Medun, Joshua B. Singer, Sam J. Wilson, Robert J. Gifford
bioRxiv 207399; doi: https://doi.org/10.1101/207399
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The evolution, distribution and diversity and of endogenous circoviral elements
Tristan P.W Dennis, William Marciel de Souza, Soledad Marsile-Medun, Joshua B. Singer, Sam J. Wilson, Robert J. Gifford
bioRxiv 207399; doi: https://doi.org/10.1101/207399

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