Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements

Genetica

Volumn 107, Issue 1-3, 1999, Pages 3-13

  Jordan, I King ^a   McDonald, John F ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NONE

Author keywords

Genomics; Molecular evolution; Retrotransposons; Selection; Ty elements

Indexed keywords

SACCHAROMYCES CEREVISIAE;

FUNGAL DNA; RNA DIRECTED DNA POLYMERASE;

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; GENETIC RECOMBINATION; GENETICS; GENOME; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; TRANSPOSON;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; DNA, FUNGAL; EVOLUTION, MOLECULAR; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; RECOMBINATION, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA-DIRECTED DNA POLYMERASE; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0033288564     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1004022704701     Document Type: Article

References (31)

1. Abbott, A., J. Abu-Threideh, C. Ahrens, R. Ainscough, E. Alexander et al., 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
2. Arkhipova, I.R., A.M. Mazo, V.A. Cherkasova, T.V. Gorelova, N.G. Schuppe et al., 1986. The steps of reverse transcription of Drosophila mobile dispersed genetic elements and U3-R-U5 structure of their LTRs. Cell 44: 555-563.
3. Blattner, F.R., G. Plunkett, III, C.A. Bloch, N.T. Perna, V. Burland et al., 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474.
4. Boeke, J.D., 1989. Transposable elements in Saccharomyces cerevisiae, pp. 335-374 in Mobile DNA, edited by D.E. Berg and M.M. Howe. American Society for Microbiology, Washington, DC.
5. Boeke, J.D., D. Eichinger, D. Castrillon & G.R. Fink, 1988. The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1. Mol. Cell. Biol. 8: 1432-1442.
6. Boeke, J.D., D.J. Garfinkel, C.A. Styles & G.R. Fink, 1985. Ty elements transpose through an RNA intermediate. Cell 40: 491-500.
7. Clare, J. & P. Farabaugh, 1985. Nucleotide sequence of a yeast Ty element: evidence for an unusual mechanism of gene expression. Proc. Natl. Acad. Sci. USA 82: 2829-2833.
8. Fink, G.R., J.D. Boeke & D.J. Garfinkel, 1986. The mechanism and consequences of retrotransposition. Trends Genet. 2: 118-123.
9. Fleischmann, R.D., M.D. Adams, O. White, R.A. Clayton, E.F. Kirkness et al., 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
10. Goffeau, A., B.G. Barrell, H. Bussey, R.W. Davis, B. Dujon et al., 1996. Life with 6000 genes. Science 274: 546, 547-563.
11. Hani, J. & H. Feldmann, 1998. tRNA genes and retroelements in the yeast genome. Nucleic Acids Res. 26: 689-696.
12. Jordan, I.K. & J.F. McDonald, 1998. Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements. J. Mol. Evol. 47: 14-20.
13. Jordan, I.K. & J.F. McDonald, 1999a. Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome. Mol. Biol. Evol. 16: 419-422.
14. Jordan, I.K. & J.F. McDonald, 1999b. The role of interelement selection in Saccharomyces cerevisiae Ty element evolution. J. Mol. Evol. 49: 352-357.
15. Jordan, I.K. & J.F. McDonald, 1999c. Tempo and mode of Ty element evolution in Saccharomyces cerevisiae. Genetics 151: 1341-1351.
16. Kim, J.M., S. Vanguri, J.D. Boeke, A. Gabriel & D.F. Voytas, 1998. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8: 464-478.
17. Koonin, E.V., A.R. Mushegian, M.Y. Galperin & D.R. Walker, 1997. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25: 619-637.
18. Matyunina, L.V., I.K. Jordan & J.F. McDonald, 1996. Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation. Proc. Natl. Acad. Sci. USA 93: 7097-7102.
19. McDonald, J.F., L.V. Matyunina, S. Wilson, I.K. Jordan, N.J. Bowen et al., 1997. LTR retrotransposons and the evolution of eukaryotic enhancers. Genetica 100: 3-13.
20. Petrov, D.A. & D.L. Hartl, 1997. Trash DNA is what gets thrown away: high rate of DNA loss in Drosophila. Gene 205: 279-289.
21. Petrov, D.A. & D.L. Hartl, 1998. High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Mol. Biol. Evol. 15: 293-302.
22. Petrov, D.A., E.R. Lozovskaya & D.L. Hartl, 1996. High intrinsic rate of DNA loss in Drosophila. Nature 384: 346-349.
23. Promislow, D.E., I.K. Jordan & J.F. McDonald, 1999. Genomic demography: a life-history analysis of transposable element evolution. Proc. R. Soc. Lond. B Biol. Sci. 266: 1555-1560.
24. Rivera, M.C., R. Jain, J.E. Moore & J.A. Lake, 1998. Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. USA 95: 6239-6244.
25. Sandmeyer, S., 1998. Targeting transposition: at home in the genome. Genome Res. 8: 416-418.
26. SanMiguel, P., A. Tikhonov, YK. Jin, N. Motchoulskaia, D. Zakharov et al., 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
27. Smit, A.F., 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6: 743-748.
28. Tatusov, R.L., E.V. Koonin & D.J. Lipman, 1997. A genomic perspective on protein families. Science 278: 631-637.
29. Voytas, D.E. & J.D. Boeke, 1992. Yeast retrotransposon revealed. Nature 358: 717.
30. Voytas, D.E. & J.D. Boeke, 1993. Yeast retrotransposons and tRNAs. Trends Genet. 9: 421-427.
31. Wickner, R.B., 1996. Viruses of yeast, fungi & parasitic microorganisms, pp. 425-453 in Fundamental Virology, edited by B.N. Fields, D.M. Knipe and P.M. Howley. Lippincott-Raven Publishers, Philadelphia.