title: Identification and classification of endogenous retroviruses in the canine genome using degenerative PCR and in-silico data analysis.
abstract: Pooled genomic DNA from 10 dogs was subjected to polymerase chain reaction with primers targeting the retroviral pro/pol region. Sequence analysis of 120 clones obtained by PCR revealed 81 of retroviral origin. Subsequent analysis of the dog genome (CanFam 2.0) by BLAST investigation using degenerate PCR products and previously identified retroviral sequences permitted the identification of additional retroviral γ and β sequences. A phylogenetic analysis using the retroviral protease (PR) and reverse transcriptase (RT) sequences in the dog genome resulted in identification of 17 γ and 7 β families. In addition, we also identified 167 spuma-like ERV elements from CanFam 2.0 based on sequence homology to murine (Mu)ERV-L and human (H)ERV-L. Our results could contribute to the understanding of the influence of retroviruses in shaping the genome structure and altering gene expression by providing quantitative and locational information of ERV loci and their diversity in the dog genome.
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Hwayang-dong, Kwangjin-gu, Seoul, South Korea. hi458@konkuk.ac.kr
authors.forename: Haiin
authors.initials: H
authors.lastname: Jo
authors.forename: Hojun
authors.initials: H
authors.lastname: Choi
authors.forename: Min-Kyeung
authors.initials: MK
authors.lastname: Choi
authors.forename: Ning
authors.initials: N
authors.lastname: Song
authors.forename: Jin-Hoi
authors.initials: JH
authors.lastname: Kim
authors.forename: Jae-Wook
authors.initials: JW
authors.lastname: Oh
authors.forename: Kunho
authors.initials: K
authors.lastname: Seo
authors.forename: Han Geuk
authors.initials: HG
authors.lastname: Seo
authors.forename: Taehoon
authors.initials: T
authors.lastname: Chun
authors.forename: Tae-Hun
authors.initials: TH
authors.lastname: Kim
authors.forename: Chankyu
authors.initials: C
authors.lastname: Park
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030121:Betaretrovirus / Q000145:classification / Q000235:genetics*; D004285:Dogs / Q000235:genetics* / Q000821:virology*; D020077:Endogenous Retroviruses / Q000145:classification / Q000235:genetics*; D017988:Gammaretrovirus / Q000145:classification / Q000235:genetics*; D016678:Genome; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods / Q000662:veterinary*; D012984:Software; D016092:Spumavirus / Q000145:classification / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D014764:Viral Proteins