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 not correlateBackground: 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.…
Verfasserangaben: | Stefanie HartmannORCiDGND, Natascha Hasenkamp, Jens Mayer, Johan Michaux, Serge Morand, Camila J. Mazzoni, Alfred L. Roca, Alex D. Greenwood |
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DOI: | https://doi.org/10.1186/s12864-015-1766-z |
ISSN: | 1471-2164 |
Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/26282858 |
Titel des übergeordneten Werks (Englisch): | BMC genomics |
Verlag: | BioMed Central |
Verlagsort: | London |
Publikationstyp: | Wissenschaftlicher Artikel |
Sprache: | Englisch |
Datum der Erstveröffentlichung: | 18.08.2015 |
Erscheinungsjahr: | 2015 |
Datum der Freischaltung: | 27.03.2017 |
Freies Schlagwort / Tag: | Endogenous retrovirus; Genomic evolution; Markov cluster algorithm; Murine leukemia virus; XMRV; Xpr1 |
Band: | 16 |
Aufsatznummer: | 613 |
Seitenanzahl: | 13 |
Fördernde Institution: | University of Saarland; DFG; National Institute of General Medical Sciences (NIGMS) [R01GM092706] |
Organisationseinheiten: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie |
DDC-Klassifikation: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
Peer Review: | Referiert |
Publikationsweg: | Open Access / Gold Open-Access |
Lizenz (Deutsch): | CC-BY - Namensnennung 4.0 International |
Externe Anmerkung: | Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1329 |