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

Abstract

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.

• Authors: Stefanie Hartmann, Natascha Hasenkamp, Jens Mayer, Johan Michaux, Serge Morand, Camila J Mazzoni, Alfred L Roca, Alex D Greenwood
• Journal: BMC genomics (BMC Genomics) Vol. 16 Pg. 613 (Aug 18 2015) ISSN: 1471-2164 [Electronic] England
• PMID: 26282858 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)

Chemical References

• RNA, Viral
• XPR1 protein, human
• Xenotropic and Polytropic Retrovirus Receptor
• Xpr1 protein, mouse

Topics

• Animals
• Europe
• Evolution, Molecular
• Gene Flow
• Leukemia Virus, Murine (classification, genetics, isolation & purification)
• Markov Chains
• Mice
• RNA, Viral (analysis)
• Sequence Analysis, RNA (methods)
• Xenotropic and Polytropic Retrovirus Receptor
• Xenotropic murine leukemia virus-related virus (genetics)