title: Prototype endogenous avian retroviruses of the genus Gallus.
abstract: Ancient endogenous retroviruses (ERVs), designated endogenous avian retrovirus (EAVs), are present in all Gallus spp. including the chicken, and resemble the modern avian sarcoma and leukosis viruses (ASLVs). The EAVs comprise several distinct retroviruses, including EAV-0, EAV-E51 and EAV-HP, as well as a putative member previously named the avian retrotransposon of chickens (ART-CH). Thus far, only the EAV-HP elements have been well characterized. Here, we determined sequences of representative EAV-0 and EAV-E51 proviruses by cloning and data mining of the 2011 assembly of the Gallus gallus genome. Although the EAV-0 elements are primarily deleted in the env region, we identified two complete EAV-0 env genes within the G. gallus genome and prototype elements sharing identity with an EAV-E51-related clone previously designated EAV-E33. Prototype EAV-0, EAV-E51 and EAV-E33 gag, pol and env gene sequences used for phylogenetic analysis of deduced proteins showed that the EAVs formed three distinct clades, with EAV-0 sharing the last common ancestor with the ASLVs. The EAV-E51 clade showed the greatest level of divergence compared with other EAVs or ASLVs, suggesting that these ERVs represented exogenous retroviruses that evolved and integrated into the germline over a long period of time. Moreover, the degree of divergence between the chicken and red jungle fowl EAV-E51 sequences suggested that they were more ancient than the other EAVs and may have diverged through mutations that accumulated post-integration. Finally, we showed that the ART-CH elements were chimeric defective ERVs comprising portions of EAV-E51 and EAV-HP rather than authentic retrotransposons.
authors.affiliation: Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92834-6850, USA.
authors.forename: Melanie Ann
authors.initials: MA
authors.lastname: Sacco
authors.affiliation: Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, UK.
authors.forename: Venugopal K
authors.initials: VK
authors.lastname: Nair
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001354:Avian Leukosis Virus / Q000235:genetics*; D001358:Avian Sarcoma Viruses / Q000235:genetics*; D001483:Base Sequence; D005075:Biological Evolution; D002645:Chickens / Q000235:genetics / Q000821:virology*; D004279:DNA, Viral / Q000235:genetics; D030561:Databases, Nucleic Acid; D020077:Endogenous Retroviruses / Q000235:genetics*; D015683:Gene Products, gag / Q000235:genetics; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D004279:DNA, Viral; D015683:Gene Products, gag; D018626:Retroelements