title: Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline [corrected].
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.
authors.affiliation: Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2.
authors.forename: K
authors.initials: K
authors.lastname: Rutherford
authors.affiliation: Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2 Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp 2000, Belgium.
authors.forename: C J
authors.initials: CJ
authors.lastname: Meehan
authors.affiliation: Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2 Dalhousie University, Faculty of Medicine, Department of Pharmacology, 5850 College St, Halifax, NS, Canada, B3H 4R2.
authors.forename: M G I
authors.initials: MG
authors.lastname: Langille
authors.affiliation: EW GROUP, 1 Hogenboegen, Visbek, Germany.
authors.forename: S G
authors.initials: SG
authors.lastname: Tyack
authors.affiliation: EW GROUP, 1 Hogenboegen, Visbek, Germany.
authors.forename: J C
authors.initials: JC
authors.lastname: McKay
authors.affiliation: Dalhousie University, Faculty of Agriculture, Department of Plant and Animal Sciences, Box 550, Truro, NS, B2N 5E3.
authors.forename: N L
authors.initials: NL
authors.lastname: McLean
authors.affiliation: Dalhousie University, Faculty of Agriculture, Department of Plant and Animal Sciences, Box 550, Truro, NS, B2N 5E3.
authors.forename: K
authors.initials: K
authors.lastname: Benkel
authors.affiliation: Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2 rbeiko@dal.ca.
authors.forename: R G
authors.initials: RG
authors.lastname: Beiko
authors.affiliation: Dalhousie University, Faculty of Agriculture, Department of Plant and Animal Sciences, Box 550, Truro, NS, B2N 5E3.
authors.forename: B
authors.initials: B
authors.lastname: Benkel
mesh_terms: D000818:Animals; D001353:Avian Leukosis / Q000821:virology*; D001354:Avian Leukosis Virus / Q000235:genetics* / Q000502:physiology; D002645:Chickens; D059014:High-Throughput Nucleotide Sequencing / Q000662:veterinary*; D011201:Poultry Diseases / Q000821:virology*; D011533:Proviruses / Q000235:genetics* / Q000502:physiology; D012984:Software
keywords: avian leukosis virus subgroup E; endogenous retroviruses; junction fragments; targeted next-generation sequencing; transposable elements