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Tempo and mode of ERV-K evolution in human and chimpanzee genomes

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Summary.

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 × 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.

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  1. Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute – ICB II, University of São Paulo, São Paulo, Brazil

    C. M. Romano, R. F. Ramalho & P. M. de A. Zanotto

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  1. C. M. Romano
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  2. R. F. Ramalho
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  3. P. M. de A. Zanotto
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Romano, C., Ramalho, R. & Zanotto, P. Tempo and mode of ERV-K evolution in human and chimpanzee genomes. Arch Virol 151, 2215–2228 (2006). https://doi.org/10.1007/s00705-006-0792-1

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