title: Tempo and mode of ERV-K evolution in human and chimpanzee genomes.
abstract: Several families of endogenous retrovirus (ERV) exist in copious numbers in the genomes of primate species. Therefore, we undertook a systematic search for endogenous retrovirus sequences from the ERV-K family, comparing across both human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes. Using conserved motifs of the ERV-K as query we identified and characterized 76 complete ERV-K elements, 54 in human (HERV-K), 34 of which were described previously, and 21 in the chimpanzee (CERV-K). Phylogenetic analysis using coding regions and LTRs showed the existence of two main branches. Group I was the most heterogeneous and had an average integration time of 18.3 MYBP (million years before present), using rates ranging from 1.5 to 4.0 x 10(-9) s/s/y (substitution per site per year). Group O/N integrated around 19.4 MYBP and nested Group N integrated about 14 MYBP. We found evidence for strong positive selection on the gag, pol and env coding regions and for A/T hypermutation. Our data suggest that the endogenous elements were possibly involved in chromosomal rearrangements and retained a great deal of information from their active stage, most likely as a consequence of host interactions. This study also contributes to the annotation effort of both human and chimpanzee genomes.
authors.affiliation: Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute - ICB II, University of São Paulo, São Paulo, Brazil.
authors.forename: C M
authors.initials: CM
authors.lastname: Romano
authors.forename: R F
authors.initials: RF
authors.lastname: Ramalho
authors.forename: P M de A
authors.initials: PM
authors.lastname: Zanotto
mesh_terms: D000818:Animals; D020077:Endogenous Retroviruses / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D015894:Genome, Human; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D002679:Pan troglodytes / Q000821:virology*; D010802:Phylogeny; D011533:Proviruses / Q000235:genetics; D017422:Sequence Analysis, DNA