Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads

Tobias Mourier*, Sarah Mollerup, Lasse Vinner, Thomas Arn Hansen, Kristín Rós Kjartansdóttir, Tobias Guldberg Frøslev, Torsten Snogdal Boutrup, Lars Peter Nielsen, Eske Willerslev, Anders J. Hansen

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

From Illumina sequencing of DNA from brain and liver tissue from the lion, Panthera leo, and tumor samples from the pike-perch, Sander lucioperca, we obtained two assembled sequence contigs with similarity to known retroviruses. Phylogenetic analyses suggest that the pike-perch retrovirus belongs to the epsilonretroviruses, and the lion retrovirus to the gammaretroviruses. To determine if these novel retroviral sequences originate from an endogenous retrovirus or from a recently integrated exogenous retrovirus, we assessed the genetic diversity of the parental sequences from which the short Illumina reads are derived. First, we showed by simulations that we can robustly infer the level of genetic diversity from short sequence reads. Second, we find that the measures of nucleotide diversity inferred from our retroviral sequences significantly exceed the level observed from Human Immunodeficiency Virus infections, prompting us to conclude that the novel retroviruses are both of endogenous origin. Through further simulations, we rule out the possibility that the observed elevated levels of nucleotide diversity are the result of co-infection with two closely related exogenous retroviruses.

Original languageEnglish (US)
Article number15644
JournalScientific Reports
Volume5
DOIs
StatePublished - Oct 23 2015

ASJC Scopus subject areas

  • General

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