Characterization of a full-length endogenous beta-retrovirus, EqERV-beta1, in the genome of the horse (Equus caballus)

Viruses

Volumn 3, Issue 6, 2011, Pages 620-628

  van der Kuyl, Antoinette C ^a  

^a ACADEMIC MEDICAL CENTER   (Netherlands)

Author keywords

Beta retrovirus; Endogenous virus; Equus caballus; Full length; Horse

Indexed keywords

CONTIG; SUPERANTIGEN;

ARTICLE; CHROMOSOME 10; CHROMOSOME 20; CHROMOSOME 21; CHROMOSOME 5; CHROMOSOME 7; ENDOGENOUS RETROVIRUS; ENVELOPE GENE; EQUUS ENDOGENOUS RETROVIRUS BETA1; FEMALE; LONG TERMINAL REPEAT; MARE; MOLECULAR PHYLOGENY; MOUSE MAMMARY TUMOR ONCOVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRO GENE; PROVIRUS; RIBOSOMAL FRAMESHIFTING; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; START CODON; STOP CODON; STRUCTURAL GENE; VIRUS CHARACTERIZATION; VIRUS DNA CELL DNA INTERACTION; VIRUS GENE; VIRUS GENOME; X CHROMOSOME;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BETARETROVIRUS; CATTLE; CHROMOSOMES, MAMMALIAN; ENDOGENOUS RETROVIRUSES; GENES, POL; GENOME; HORSES; MICE; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; PROVIRUSES; SEQUENCE ALIGNMENT; TERMINAL REPEAT SEQUENCES; VIRUS INTEGRATION;

BOS; BOS TAURUS; EQUIDAE; EQUUS CABALLUS; MOUSE MAMMARY TUMOR VIRUS; MURINAE;

EID: 79959664564     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v3060620     Document Type: Article

References (25)

1. Horie, M.; Honda, T.; Suzuki, Y.; Kobayashi, Y.; Daito, T.; Oshida, T.; Ikuta, K.; Jern, P.; Gojobori, T.; Coffin, J.M.; Tomonaga, K. Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 2010, 463, 84-87.
2. Belyi, V.A.; Levine, A.J.; Skalka, A.M. Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes. PLoS. Pathog. 2010, 6, e1001030.
3. Taylor, D.J.; Leach, R.W.; Bruenn, J. Filoviruses are ancient and integrated into mammalian genomes. BMC. Evol. Biol. 2010, 10, 193.
4. Tanaka-Taya, K.; Sashihara, J.; Kurahashi, H.; Amo, K.; Miyagawa, H.; Kondo, K.; Okada, S.; Yamanishi, K. Human herpesvirus 6 (HHV-6) is transmitted from parent to child in an integrated form and characterization of cases with chromosomally integrated HHV-6 DNA. J. Med. Virol. 2004, 73, 465-473.
5. Weiss, R.A. The discovery of endogenous retroviruses. Retrovirology. 2006, 3, 67.
6. Jern, P.; Sperber, G.O.; Blomberg, J. Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology. 2005, 2, 50.
7. Gifford, R.J.; Katzourakis, A.; Tristem, M.; Pybus, O.G.; Winters, M.; Shafer, R.W. 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, 20362-20367.
8. van der Loo W; Abrantes, J.; Esteves, P.J. Sharing of endogenous lentiviral gene fragments among leporid lineages separated for more than 12 million years. J. Virol. 2009, 83, 2386-2388.
9. Keckesova, Z.; Ylinen, L.M.; Towers, G.J.; Gifford, R.J.; 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, 7-11.
10. Greenwood, A.D.; Lee, F.; Capelli, C.; DeSalle, R.; Tikhonov, A.; Marx, P.A.; MacPhee, R.D. Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives. Mol. Biol. Evol. 2001, 18, 840-847.
11. Benit, L.; Lallemand, J.B.; Casella, J.F.; Philippe, H.; Heidmann, T. ERV-L elements: a family of endogenous retrovirus-like elements active throughout the evolution of mammals. J. Virol. 1999, 73, 3301-3308.
12. Wade, C.M.; Giulotto, E.; Sigurdsson, S.; Zoli, M.; Gnerre, S.; Imsland, F.; Lear, T.L.; Adelson, D.L.; Bailey, E.; Bellone, R.R.; et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 2009, 326, 865-867.
13. Horse (Equus caballus) Genome Browser Gateway of the Genome Bioinformatics Group of UC Santa Cruz. Available online: http://genome.ucsc.edu/cgi-bin/hgGateway?db=equCab2 (accessed on 4 January 2011).
14. Horse Genome Resources, NCBI. Available online: http://www.ncbi.nlm.nih.gov/projects/genome/guide/horse/ (accessed on 8 November 2010).
15. NCBI Basic Local Alignment Search Tool BLAST. Available online: http://blast.ncbi.nlm.nih.gov/ (accessed on 8 November 2010).
16. NCBI nucleotide database. Available online: www.ncbi.nlm.nih.gov/nucleotide/ (accessed on 8 November 2010).
17. BioEdit Sequence Alignment Editor, Version 7.0.9. Available online: www.mbio.ncsu.edu/BioEdit/bioedit.html (accessed on 14 October 2010).
18. MEGA 4 software package. Available online: www.megasoftware.net (accessed on 14 October 2010).
19. Marquet, R.; Isel, C.; Ehresmann, C.; Ehresmann, B. tRNAs as primer of reverse transcriptases. Biochimie 1995, 77, 113-124.
20. Shimotohno, K.; Mizutani, S.; Temin, H.M. Sequence of retrovirus provirus resembles that of bacterial transposable elements. Nature 1980, 285, 550-554.
21. Durbin, R.M.; Abecasis, G.R.; Altshuler, D.L.; Auton, A.; Brooks, L.D.; Durbin, R.M.; Gibbs, R.A.; Hurles, M.E.; McVean, G.A. A map of human genome variation from population-scale sequencing. Nature 2010, 467, 1061-1073.
22. Benachenhou, F.; Jern, P.; Oja, M.; Sperber, G.; Blikstad, V.; Somervuo, P.; Kaski, S.; Blomberg, J. Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data. PLoS. ONE 2009, 4, e5179.
23. Mayer, J.; Meese, E.U. Presence of dUTPase in the various human endogenous retrovirus K (HERV-K) families. J. Mol. Evol. 2003, 57, 642-649.
24. van der Kuyl, A.C.; Mang, R.; Dekker, J.T.; Goudsmit, J. Complete nucleotide sequence of simian endogenous type D retrovirus with intact genome organization: evidence for ancestry to simian retrovirus and baboon endogenous virus. J. Virol. 1997, 71, 3666-3676.
25. Marchler-Bauer, A.; Anderson, J.B.; Chitsaz, F.; Derbyshire, M.K.; Weese-Scott, C.; Fong, J.H.; Geer, L.Y.; Geer, R.C.; Gonzales, N.R.; Gwadz, M.; et al. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 2009, 37, D205-D210.