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Comparing PreXMRV-2 gag sequence diversity in laboratory and wild mice using deep sequencing.
Jens Mayer1, Camila J Mazzoni, Alex D Greenwood
1Department of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, 66421 Homburg, Germany.
Virus Research
|July 10, 2012
Summary
Parts of the xenotropic murine leukemia virus-related virus (XMRV) genome, termed PreXMRV-2, are naturally present in wild and laboratory mice. Deep sequencing reveals these retroviral sequences are widespread within the Mus musculus lineage.
Area of Science:
- Virology
- Genomics
- Evolutionary Biology
Background:
- The xenotropic murine leukemia virus-related virus (XMRV) is a recently identified retrovirus.
- XMRV is believed to be a laboratory recombinant, but related sequences (PreXMRV-2) have been found in mouse genomes.
- This suggests that components of the XMRV genome may originate from naturally occurring murine retroviruses.
Purpose of the Study:
- To investigate the diversity and distribution of PreXMRV-2 gag sequences in wild and laboratory mice.
- To compare these sequences with previously reported XMRV-like sequences.
- To understand the evolutionary relationships and prevalence of these endogenous retroviral elements.
Main Methods:
- Genomic DNA extraction from wild and inbred laboratory mouse strains.
- High-throughput amplicon sequencing targeting PreXMRV-2 gag sequences.
- Phylogenetic analysis of identified sequences.
- Comparison with Sanger sequencing results.
Main Results:
- PreXMRV-2 gag sequences, including a specific 24 nt deletion, were frequently detected in various wild mice and laboratory mouse strains.
- These sequences were found within a high background of non-XMRV-like sequences.
- Phylogenetic analysis indicated that PreXMRV-2 gag sequences from mice, cell lines, and patient samples form a single, evolutionarily young clade.
- The sequences are diverse and widespread in Mus musculus domesticus and derived laboratory mice, but not found outside this lineage.
- Deep sequencing proved more effective than Sanger sequencing for detecting these diverse retroviral sequences.
Conclusions:
- PreXMRV-2 sequences are naturally occurring and widespread endogenous retroviral elements in Mus musculus.
- These findings suggest a natural origin for parts of the XMRV genome within the mouse lineage.
- Deep sequencing is crucial for accurate detection and analysis of diverse and low-prevalence retroviral sequences in complex genomes.
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