title: Endogenous avian leukosis viral loci in the Red Jungle Fowl genome assembly.
abstract: The current build (galGal4) of the genome of the ancestor of the modern chicken, the Red Jungle Fowl, contains a single endogenous avian leukosis viral element (ALVE) on chromosome 1 (designated RSV-LTR; family ERVK). The assembly shows the ALVE provirus juxtaposed with a member of a second family of avian endogenous retroviruses (designated GGERV20; family ERVL); however, the status of the 3' end of the ALVE element as well as its flanking region remain unclear due to a gap in the reference genome sequence. In this study, we filled the gap in the assembly using a combination of long-range PCR (LR-PCR) and a short contig present in the unassembled portion of the reference genome database. Our results demonstrate that the ALVE element (ALVE-JFevB) is inserted into the putative envelope region of a GGERV20 element, roughly 1 kbp from its 3' end, and that ALVE-JFevB is complete, and depending on its expression status, potentially capable of directing the production of virus. Moreover, the unassembled portion of the genome database contains junction fragments for a second, previously characterized endogenous proviral element, ALVE-6.
authors.affiliation: Dalhousie University, Department of Plant and Animal Sciences, Box 550, Truro, Nova Scotia, Canada, B2N 5E3 bbenkel@dal.ca.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Benkel
authors.affiliation: Dalhousie University, Department of Plant and Animal Sciences, Box 550, Truro, Nova Scotia, Canada, B2N 5E3.
authors.forename: Katherine
authors.initials: K
authors.lastname: Rutherford
mesh_terms: D000818:Animals; D001354:Avian Leukosis Virus / Q000235:genetics*; D002645:Chickens / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics*; D020077:Endogenous Retroviruses / Q000235:genetics*; D005260:Female; D016678:Genome; D016133:Polymerase Chain Reaction
chemical_list: D004279:DNA, Viral
keywords: Red Jungle Fowl; avian leukosis virus; endogenous retrovirus; reference genome