Improved integration time estimation of endogenous retroviruses with phylogenetic data

PLoS ONE

Volumn 6, Issue 3, 2011, Pages

  Martins, Hugo ^a,b   Villesen, Palle ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; ENDOGENOUS RETROVIRUS; GENE SEQUENCE; LONG TERMINAL REPEAT; MOLECULAR CLOCK; MOLECULAR EVOLUTION; MONTE CARLO METHOD; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIMATE; PROBABILITY; SPECIES DIFFERENTIATION; STATISTICAL MODEL; TIME; VIRUS GENE; GENETIC VARIABILITY; GENETICS; HUMAN; SPECIES DIFFERENCE; VIRUS DNA CELL DNA INTERACTION;

MAMMALIA; PRIMATES;

ENDOGENOUS RETROVIRUSES; GENETIC VARIATION; HUMANS; MARKOV CHAINS; MONTE CARLO METHOD; PHYLOGENY; SPECIES SPECIFICITY; TERMINAL REPEAT SEQUENCES; TIME FACTORS; VIRUS INTEGRATION;

EID: 79952327304     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014745     Document Type: Article

References (28)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
2. Blond JL, Lavillette D, Cheynet V, Bouton O, Oriol G, et al. (2000) An envelope glycoprotein of the human endogenous retrovirus HERV-W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor. J Virol 74 (7): 3321-3329.
3. Mi S, Lee X, Li X, Veldman GM, Finnerty H, et al. (2000) Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 403 (6771): 785-789.
4. Blaise S, de Parseval N, Benit L, Heidmann T, (2003) Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. Proc Natl Acad Sci USA 100 (22): 13013-13018.
5. Prudhomme S, Bonnaud B, Mallet F, (2005) Endogenous retroviruses and animal reproduction. Cytogenet Genome Res 110 (1-4): 353-64.
6. Antony JM, van Marle G, Opii W, Butterfield DA, Mallet F, et al. (2004) Human endogenous retrovirus glycoprotein-mediated induction of redox reactants causes oligodendrocyte death and demyelination. Nat Neurosci 7 (10): 1088-1095.
7. Sotgiu S, Arru G, Mameli G, Serra C, Pugliatti M, et al. (2006) Multiple sclerosis-associated retrovirus in early multiple sclerosis: a six-year follow-up of a Sardinian cohort. Mult Scler 12 (6): 698-703.
8. Ruprecht K, Mayer J, Sauter M, Roemer K, Mueller-Lantzsch N, (2008) Endogenous retroviruses and cancer. Cell Mol Life Sci. 65 (21): 3366-82.
9. Doolitle RF, Feng DF, Johnson MS, McClure MA, (1989) Origins and evolutionary relationships of retroviruses. Q Rev Biol 64: 1-30.
10. Coffin JM: Structure and Classification of Retroviruses. in Levy JA The Retroviridae (1st ed.) New York: Plenum Pres.
11. Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, et al. (2004) Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci USA 101 (14): 4984-99.
12. Jern P, Sperber GO, Blomberg J, (2005) Use of Endogenous Retroviral Sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology 2: 50.
13. Gilboa E, Mitra SW, Goff S, Baltimore DA, (1979) Detailed model of reverse transcrption and tests of crucial aspects. Cell 18: 93-100.
14. Schrago CG, Russo CA, (2003) Timing the origin of New World monkeys. Mol Biol Evol 20 (10): 1620-5.
15. Romano CM, Ramalho CF, de A Zanotto PM, (2006) Tempo and mode of ERV-K evolution in human and chimpanzee genomes. Archives of Virology 151: 2215-2228.
16. Romano CM, de Melo FL, Corsini MAB, Holmes EC, de A Zanotto PM, (2007) Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys. PLoS ONE 2 (10): e1026.
17. Hervé CA, Forrest G, Löwer R, Griffiths DJ, Venables PJ, (2004) Conservation and loss of the ERV3 open reading frame in primates. Genomics 83 (5): 940-943.
18. Aagaard L, Villesen P, Kjeldbjerg AL, Pedersen FS, (2005) The approximately 30-million-year-old ERVPb1 envelope gene is evolutionarily conserved among hominoids and Old World Monkeys. Genomics 86 (6): 685-691.
19. Blond JL, Beseme F, Duret L, Bouton O, Bedin F, et al. (1999) Molecular characterization and placental expression of HERV-W, a new human endogenous retrovirus family. J Virol 73: 1175-1185.
20. Blaise S, Ruggieri A, Dewannieux M, Cosset FL, Heidmann T, (2004) Identification of an envelope protein from the FRD family of Human Endogenous Retroviruses (HERV-FRD) conferring infectivity and functional conservation among simians. J Virol 78: 1050-1054.
21. Dupressoir A, Marceau G, Vernochet C, Bénit L, Kanellopoulos C, et al. (2005) Syncytin-A and Syncytin-B, two fusogenic placenta-specific murine envelope genes of retroviral origin conserved in Muridae. Proc Natl Acad Sci USA 102 (3): 725-30.
22. Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 36: D773-9.
23. DNA dotplot web utility,http://www.vivo.colostate.edu/molkit/dnadot/.
24. Thompson JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of the progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 (22): 4673-80.
25. Felsenstein J, (2004) PHYLIP (Phylogeny Inference Package). Version 3.6. Department of Genome Sciences, University of Washington, Seattle.
26. Yang Z, (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13 (5): 555-556.
27. Newick Utils 0.11 by Thomas Junier:http://sourceforge.net/projects/newickutils/.
28. Tamura K, Dudley J, Nei M, Kumar S, (2004) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.