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    Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline

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    Publication date
    2016-10
    Author
    Rutherford, K.
    Meehan, Conor J.
    Langille, M.G.I.
    Tyack, S.G.
    McKay, J.C.
    McLean, N.L.
    Benkel, K.
    Beiko, R.G.
    Benkel., B.
    Keyword
    Avian leukosis virus subgroup E
    Targeted next-generation sequencing
    Junction fragments
    Transposable elements
    Endogenous retroviruses
    Peer-Reviewed
    Yes
    
    Metadata
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    Abstract
    Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken.
    URI
    http://hdl.handle.net/10454/17493
    Version
    No full-text in the repository
    Citation
    Rutherford K, Meehan CJ, Langille MGI et al (2016) Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline. Poultry Science. 95(10): 2250-2258.
    Link to publisher’s version
    https://doi.org/10.3382/ps/pew194
    Type
    Article
    Collections
    Life Sciences Publications

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