The phylogeny of orthoretroviral long terminal repeats (LTRs) |
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Authors: | Farid Benachenhou Vidar BlikstadJonas Blomberg |
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Affiliation: | Section of Virology, Dept. of Medical Sciences, Uppsala University, Dag Hammarskjolds v. 17, SE-75185 Uppsala, Sweden |
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Abstract: | LTRs are sequence elements in retroviruses and retrotransposons which are difficult to align due to their variability. One way of handling such cases is to use Hidden Markov Models (HMMs). In this work HMMs of LTRs were constructed for three groups of orthoretroviruses: the betaretroviruslike human MMTV-like (HML) endogenous retroviruses, the lentiviruses, including HIV, and gammaretroviruslike human endogenous retroviruses (HERVs). The HMM-generated LTR alignments and the phylogenetic trees constructed from them were compared with trees based on alignments of the pol gene at the nucleic acid level. The majority of branches in the LTR and pol based trees had the same order for the three retroviral genera, showing that HMM methods are successful in aligning and constructing phylogenies of LTRs. The HML LTR tree deviated somewhat from the pol tree for the groups HML3, HML7 and HML6. Among the gammaretroviruslike proviruses, the exogenous Mouse Leukemia Virus (MLV) was highly related to HERV-T in the pol based tree, but not in the LTR based tree. Aside from these differences, the similarity between the trees indicates that LTRs and pol coevolved in a largely monophyletic way. |
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Keywords: | LTR, long terminal repeat HMM, Hidden Markov Model MMTV, Mouse Mammary Tumor Virus HML, human MMTV-like HERV, human endogenous retrovirus pol, polymerase gene nucleotide sequence Pol, polymerase gene amino-acid sequence Gag, group antigen amino-acid sequence ERV, human endogenous retrovirus PBS, primer binding site HIV, human immunodeficiency virus SIV, simian immunodeficiency virus LST, lhoest's monkey MND, mandrill SUN, sun-tailed macaque DRL, drill monkey RCM, red-capped mangabey CPZ, chimpanzee O.BE, O.CM, HIV-1 type O SAB, African green monkey, sabaeus subspecies SIV-VER, vervet monkey SYK, Sykes' monkey MON, Mona's monkey MUS, moustached monkey GSN, greater spot-nosed monkey DEB, DeBrazza's monkey DEN, Dent's Mona monkey COL, guereza colobus BIV, bovine immunodeficiency virus Visna, ovine maedi-visna virus FIV, feline immunodeficiency virus EIAV, equine infectious anemia virus MLV, murine leukemia virus GaLV, gibbon ape leukemia virus FLV, feline leukemia virus |
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