Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse

Background: Endogenous
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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.
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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.
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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.