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

Stefanie Hartmann, Natascha Hasenkamp, Jens Mayer, Johan Michaux, Serge Morand, Camila J. Mazzoni, Alfred L. Roca, Alex D. Greenwood

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number613
JournalBMC genomics
Volume16
Issue number1
DOIs
StatePublished - Aug 18 2015

Keywords

  • Endogenous retrovirus
  • Genomic evolution
  • Markov cluster algorithm
  • Murine leukemia virus
  • XMRV
  • Xpr1

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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    Hartmann, S., Hasenkamp, N., Mayer, J., Michaux, J., Morand, S., Mazzoni, C. J., Roca, A. L., & Greenwood, A. D. (2015). Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse. BMC genomics, 16(1), [613]. https://doi.org/10.1186/s12864-015-1766-z