Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse.
BACKGROUND
Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present.


RESULTS
Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences.


CONCLUSIONS
Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection.
Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 22-24, Potsdam, 14476, Germany. stefanie.hartmann@uni-potsdam.de.
Stefanie
S
Hartmann
Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, 24306, Germany. hasenkamp@evolbio.mpg.de.
Natascha
N
Hasenkamp
Department of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, Building 60, Homburg, 66421, Germany. jens.mayer@uniklinik-saarland.de.
Jens
J
Mayer
Centre de Biologie et de Gestion des Populations, Campus International de Baillarguet, CS 30016, Montferrier-le-Lez, 34988, France. Johan.Michaux@ulg.ac.be.
Johan
J
Michaux
Conservation Genetics Unit, Institute of Botany (B. 22), University Liège, Liège, 4000, Belgium. serge.morand@univ-montp2.fr.|CIRAD TA C- 22 / E - Campus international de Baillarguet, Montpellier Cedex 5, 34398, France. serge.morand@univ-montp2.fr.
Serge
S
Morand
Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany. mazzoni@izw-berlin.de.|Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, Berlin, 10315, Germany. mazzoni@izw-berlin.de.
Camila J
CJ
Mazzoni
Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory, Urbana, 61801, IL, USA. roca@illinois.edu.
Alfred L
AL
Roca
Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, Berlin, 10315, Germany. greenwood@izw-berlin.de.
Alex D
AD
Greenwood
D000818:Animals; D005060:Europe; D019143:Evolution, Molecular; D051456:Gene Flow; D009052:Leukemia Virus, Murine / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D008390:Markov Chains; D051379:Mice; D012367:RNA, Viral / Q000032:analysis*; D017423:Sequence Analysis, RNA / Q000379:methods*; D000089842:Xenotropic and Polytropic Retrovirus Receptor; D058008:Xenotropic murine leukemia virus-related virus / Q000235:genetics
D012367:RNA, Viral; C000715267:XPR1 protein, human; D000089842:Xenotropic and Polytropic Retrovirus Receptor; C000715268:Xpr1 protein, mouse