Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads.
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.
Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark.
Tobias
T
Mourier
Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark.
Sarah
S
Mollerup
Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark.
Lasse
L
Vinner
Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark.
Thomas Arn
TA
Hansen
Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark.
Kristín Rós
KR
Kjartansdóttir
Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark.
Tobias
T
Guldberg Frøslev
Section for Virology, National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark.
Torsten
T
Snogdal Boutrup
Department for Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark.
Lars Peter
LP
Nielsen
Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark.
Eske
E
Willerslev
Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark.
Anders J
AJ
Hansen
D000818:Animals; D020077:Endogenous Retroviruses / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D010802:Phylogeny