Improved integration time estimation of endogenous retroviruses with phylogenetic data

TY - JOUR

T1 - Improved integration time estimation of endogenous retroviruses with phylogenetic data

AU - Martins, Hugo

AU - Villesen, Palle

PY - 2011/1/1

Y1 - 2011/1/1

N2 - Endogenous retroviruses (ERVs) are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Most loci are rendered non-functional by mutations, but several intact retroviral genes are known in mammalian genomes. Some have been adopted by the host species, while the beneficial roles of others remain unclear. Besides the obvious possible immunogenic impact from transcribing intact viral genes, endogenous retroviruses have also become an interesting and useful tool to study phylogenetic relationships. The determination of the integration time of these viruses has been based upon the assumption that both 5' and 3' Long Terminal Repeats (LTRs) sequences are identical at the time of integration, but evolve separately afterwards. Similar approaches have been using either a constant evolutionary rate or a range of rates for these viral loci, and only single species data. Here we show the advantages of using different approaches.

AB - Endogenous retroviruses (ERVs) are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Most loci are rendered non-functional by mutations, but several intact retroviral genes are known in mammalian genomes. Some have been adopted by the host species, while the beneficial roles of others remain unclear. Besides the obvious possible immunogenic impact from transcribing intact viral genes, endogenous retroviruses have also become an interesting and useful tool to study phylogenetic relationships. The determination of the integration time of these viruses has been based upon the assumption that both 5' and 3' Long Terminal Repeats (LTRs) sequences are identical at the time of integration, but evolve separately afterwards. Similar approaches have been using either a constant evolutionary rate or a range of rates for these viral loci, and only single species data. Here we show the advantages of using different approaches.

U2 - 10.1371/journal.pone.0014745

DO - 10.1371/journal.pone.0014745

M3 - Journal article

C2 - 21394200

SN - 1932-6203

VL - 6

SP - e14745

JO - PLoS One

JF - PLoS One

IS - 3

ER -