Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates

Retrovirology

Volumn 11, Issue 1, 2014, Pages

  Hron, Tomáš ^a   Fábryová, Helena ^a   Pačes, Jan ^a   Elleder, Daniel ^a  

^a INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

Author keywords

Dermoptera; Endogenous lentiviruses; Paleovirology

Indexed keywords

ARTICLE; COMPUTER MODEL; DERMOPTERA; ENDOGENOUS VIRUS; ENVELOPE GENE; GAG GENE; GALEOPTERUS VARIEGATUS; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC SCREENING; LENTIVIRINAE; LENTIVIRUS INFECTION; LONG TERMINAL REPEAT; MAMMALIAN GENETICS; MOLECULAR EVOLUTION; NONHUMAN; ORF1 GENE; ORF2 GENE; ORF3 GENE; PHYLOGENY; SEQUENCE ALIGNMENT; STRUCTURAL GENE; VIRUS GENE; VIRUS IDENTIFICATION; ANIMAL; BIOLOGY; CLASSIFICATION; ENDOGENOUS RETROVIRUS; GENE ORDER; GENETICS; MALAYSIA; MAMMAL; VIROLOGY;

DERMOPTERA; LENTIVIRUS; MAMMALIA; PRIMATES; VERTEBRATA;

ANIMALS; COMPUTATIONAL BIOLOGY; ENDOGENOUS RETROVIRUSES; EVOLUTION, MOLECULAR; GENE ORDER; GENES, VIRAL; LENTIVIRUS; MALAYSIA; MAMMALS; PHYLOGENY;

EID: 84935020844     PISSN: None     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/s12977-014-0084-x     Document Type: Article

References (26)

1. Johnson WE: A proviral puzzle with a prosimian twist. Proc Natl Acad Sci U S A 2008, 105(51):20051-20052.
2. Stoye JP: Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat Rev Microbiol 2012, 10(6):395-406.
3. Katzourakis A, Tristem M, Pybus OG, Gifford RJ: Discovery and analysis of the first endogenous lentivirus. Proc Natl Acad Sci U S A 2007, 104(15):6261-6265.
4. Gifford RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW: A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc Natl Acad Sci U S A 2008, 105(51):20362-20367.
5. Gilbert C, Maxfield DG, Goodman SM, Feschotte C: Parallel germline infiltration of a lentivirus in two Malagasy lemurs. PLoS Genet 2009, 5(3):e1000425.
6. Cui J, Holmes EC: Endogenous lentiviruses in the ferret genome. J Virol 2012, 86(6):3383-3385.
7. Keckesova Z, Ylinen LM, Towers GJ, Gifford RJ, Katzourakis A: Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology 2009, 384(1):7-11.
8. Han GZ, Worobey M: Endogenous lentiviral elements in the weasel family (Mustelidae). Mol Biol Evol 2012, 29(10):2905-2908.
9. Belshaw R, Watson J, Katzourakis A, Howe A, Woolven-Allen J, Burt A, Tristem M: Rate of recombinational deletion among human endogenous retroviruses. J Virol 2007, 81(17):9437-9442.
10. Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31(13):3406-3415.
11. Kohany O, Gentles AJ, Hankus L, Jurka J: Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 2006, 7:474.
12. Petersen TN, Brunak S, Heijne G, Nielsen H: SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8:785-786.
13. Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305(3):567-580.
14. Duckert P, Brunak S, Blom N: Prediction of proprotein convertase cleavage sites. Protein Eng Des Sel 2004, 17(1):107-112.
15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28(10):2731-2739.
16. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797.
17. Dimmic MW, Rest JS, Mindell DP, Goldstein RA: rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J Mol Evol 2002, 55(1):65-73.
18. Huelsenbeck JP, Ronquist F: MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England) 2001, 17(8):754-755.
19. Johnson WE, Coffin JM: Constructing primate phylogenies from ancient retrovirus sequences. Proc Natl Acad Sci U S A 1999, 96(18):10254-10260.
20. Kumar S, Subramanian S: Mutation rates in mammalian genomes. Proc Natl Acad Sci U S A 2002, 99(2):803-808.
21. Chinwalla AT, Cook LL, Delehaunty KD, Fewell GA, Fulton LA, Fulton RS, Graves TA, Hillier LW, Mardis ER, McPherson JD, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, et al: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420(6915):520-562.
22. Janečka JE, Helgen KM, Lim NT-L, Baba M, Izawa M, Boeadi, Murphy WJ: Evidence for multiple species of Sunda colugo. Curr Biol 2008, 18(21):R1001-R1002.
23. Martin RD: Colugos: obscure mammals glide into the evolutionary limelight. J Biol 2008, 7(4):13.
24. Nie WH, Fu BY, O'Brien PCM, Wang JH, Su WT, Tanomtong A, Volobouev V, Ferguson-Smith MA, Yang FT: Flying lemurs - the 'flying tree shrews'? molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade. BMC Biol 2008, 6:11.
25. Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann A, Helgen KM, Springer MS, Murphy WJ: Molecular and genomic data identify the closest living relative of primates. Science (New York, NY) 2007, 318(5851):792-794.
26. Hedges SB, Dudley J, Kumar S: TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (Oxford, England) 2006, 22(23):2971-2972.