The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes

Dennis, T. P.W., Souza, W. M. d., Marsile-Medun, S., Singer, J. B., Wilson, S. J. and Gifford, R. J. (2018) The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. Virus Research, (doi:10.1016/j.virusres.2018.03.014) (PMID:29601845) (Early Online Publication)

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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 are a useful source of 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.

Item Type:Articles
Status:Early Online Publication
Refereed:Yes
Glasgow Author(s) Enlighten ID:Gifford, Dr Robert and Marsile-Medun, Ms Soledad and Wilson, Dr Sam and Singer, Dr Joshua and Dennis, Tristan and Souza, Mr William
Authors: Dennis, T. P.W., Souza, W. M. d., Marsile-Medun, S., Singer, J. B., Wilson, S. J., and Gifford, R. J.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Virus Research
Publisher:Elsevier
ISSN:0168-1702
ISSN (Online):1872-7492
Published Online:27 March 2018
Copyright Holders:Copyright © 2018 The Authors
First Published:First published Virus Research 2018
Publisher Policy:Reproduced under a Creative Commons License

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