Phylogeny Derived from Coding Retroviral Genome Organization |
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Authors: | Céline Renoux-Elbé Rémi Cheynier Simon Wain-Hobson |
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Institution: | (1) Unité de Rétrovirologie Moléculaire, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France, FR |
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Abstract: | When divergence between viral species is large, the analysis and comparison of nucleotide or protein sequences are dependent
on mutation biases and multiple substitutions per site leading, among other things, to the underestimation of branch lengths
in phylogenetic trees. To avoid the problem of multiply substituted sites, a method not directly based on the nucleic or protein
sequences has been applied to retroviruses. It consisted of asking questions about genome structure or organization, and gene
function, the series of answers creating coded sequences analyzed by phylogenic software. This method recovered the principal
retroviral groups such as the lentiviruses and spumaviruses and highlighted questions and answers characteristic of each group
of retroviruses. In general, there was reasonable concordance between the coded genome methodology and that based on conventional
phylogeny of the integrase protein sequence, indicating that integrase was fixing mutations slowly enough to marginalize the
problem of multiple substitutions at sites. To a first approximation, this suggests that the acquisition of novel genetic
features generally parallels the fixation of amino acid substitutions.
Received: 18 May 2001 / Accepted: 7 September 2001 |
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Keywords: | : Retrovirus — Virus evolution — Genome organization — Phylogeny — Phylogenetic bias |
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