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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 notBackground: 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.…
Author details: | Stefanie HartmannORCiDGND, Natascha Hasenkamp, Jens MayerORCiD, Johan Michaux, Serge MorandORCiD, Camila J. Mazzoni, Alfred L. Roca, Alex D. GreenwoodORCiD |
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URN: | urn:nbn:de:kobv:517-opus4-431200 |
DOI: | https://doi.org/10.25932/publishup-43120 |
ISSN: | 1866-8372 |
Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/26282858 |
Title of parent work (German): | Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe |
Publication series (Volume number): | Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (1329) |
Publication type: | Postprint |
Language: | English |
Date of first publication: | 2015/08/18 |
Publication year: | 2015 |
Publishing institution: | Universität Potsdam |
Release date: | 2023/06/23 |
Tag: | Markov cluster algorithm; XMRV; Xpr1; endogenous retrovirus; genomic evolution; murine leukemia virus |
Issue: | 1329 |
Number of pages: | 13 |
Source: | BMC Genomics 16 (2015) Art. 613. DOI: https://doi.org/10.1186/s12864-015-1766-z |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie |
DDC classification: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
Peer review: | Referiert |
Publishing method: | Open Access / Green Open-Access |
License (German): | CC-BY - Namensnennung 4.0 International |
External remark: | Bibliographieeintrag der Originalveröffentlichung/Quelle |