Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae (original) (raw)

References

  1. Ohno, S. Evolution by Gene Duplication (Allen and Unwin, London, 1970)
    Google Scholar
  2. Mayer, V. W. & Aguilera, A. High levels of chromosome instability in polyploids of Saccharomyces cerevisiae. Mutat. Res. 231, 177–186 (1990)
    CAS PubMed Google Scholar
  3. Wolfe, K. H. & Shields, D. C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708–713 (1997)
    ADS CAS PubMed Google Scholar
  4. Seoighe, C. & Wolfe, K. H. Updated map of duplicated regions in the yeast genome. Gene 238, 253–261 (1999)
    CAS PubMed Google Scholar
  5. Melnick, L. & Sherman, F. The gene clusters ARC and COR on chromosomes 5 and 10, respectively, of Saccharomyces cerevisiae share a common ancestry. J. Mol. Biol. 233, 372–388 (1993)
    CAS PubMed Google Scholar
  6. Goffeau, A. et al. Life with 6000 genes. Science 274, 546, 563–567 (1996)
    ADS CAS PubMed Google Scholar
  7. Philippsen, P. et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications. Nature 387, 93–98 (1997)
    CAS PubMed Google Scholar
  8. Mewes, H. W. et al. Overview of the yeast genome. Nature 387, 7–65 (1997)
    PubMed Google Scholar
  9. Coissac, E., Maillier, E. & Netter, P. A comparative study of duplications in bacteria and eukaryotes: the importance of telomeres. Mol. Biol. Evol. 14, 1062–1074 (1997)
    CAS PubMed Google Scholar
  10. Friedman, R. & Hughes, A. L. Gene duplication and the structure of eukaryotic genomes. Genome Res. 11, 373–381 (2001)
    CAS PubMed PubMed Central Google Scholar
  11. Hughes, T. R. et al. Widespread aneuploidy revealed by DNA microarray expression profiling. Nature Genet. 25, 333–337 (2000)
    CAS PubMed Google Scholar
  12. Piskur, J. Origin of the duplicated regions in the yeast genomes. Trends Genet. 17, 302–303 (2001)
    CAS PubMed Google Scholar
  13. Koszul, R., Caburet, S., Dujon, B. & Fischer, G. Eukaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J. 23, 234–243 (2004)
    CAS PubMed Google Scholar
  14. Llorente, B. et al. Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae. FEBS Lett. 487, 101–112 (2000)
    CAS PubMed Google Scholar
  15. Llorente, B. et al. Genomic exploration of the hemiascomycetous yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae. FEBS Lett. 487, 122–133 (2000)
    CAS PubMed Google Scholar
  16. Wong, S., Butler, G. & Wolfe, K. H. Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc. Natl Acad. Sci. USA 99, 9272–9277 (2002)
    ADS CAS PubMed PubMed Central Google Scholar
  17. Langkjaer, R. B., Cliften, P. F., Johnston, M. & Piskur, J. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 421, 848–852 (2003)
    ADS CAS PubMed Google Scholar
  18. Kurtzman, C. P., Lynch, M. & Force, A. Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. FEMS Yeast Res. 4, 233–245 (2003)
    CAS Google Scholar
  19. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254 (2003)
    ADS CAS PubMed Google Scholar
  20. Lynch, M. & Force, A. The probability of duplicate gene preservation by subfunctionalization. Genetics 154, 459–473 (2000)
    CAS PubMed PubMed Central Google Scholar
  21. Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1545 (1999)
    CAS PubMed PubMed Central Google Scholar
  22. Kondrashov, F. A., Rogozin, I. B., Wolf, Y. I. & Koonin, E. V. Selection in the evolution of gene duplications. Genome Biol. 3, RESEARCH0008.1–0008.9 (2002)
  23. Shore, D., Squire, M. & Nasmyth, K. A. Characterization of two genes required for the position-effect control of yeast mating-type genes. EMBO J. 3, 2817–2823 (1984)
    CAS PubMed PubMed Central Google Scholar
  24. Bell, S. P., Kobayashi, R. & Stillman, B. Yeast origin recognition complex functions in transcription silencing and DNA replication. Science 262, 1844–1849 (1993)
    ADS CAS PubMed Google Scholar
  25. Benard, L., Carroll, K., Valle, R. C., Masison, D. C. & Wickner, R. B. The ski7 antiviral protein is an EF1-alpha homolog that blocks expression of non-Poly(A) mRNA in Saccharomyces cerevisiae. J. Virol. 73, 2893–2900 (1999)
    CAS PubMed PubMed Central Google Scholar
  26. Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003)
    ADS CAS PubMed Google Scholar
  27. Sanz, M., Trilla, J. A., Duran, A. & Roncero, C. Control of chitin synthesis through Shc1p, a functional homologue of Chs4p specifically induced during sporulation. Mol. Microbiol. 43, 1183–1195 (2002)
    CAS PubMed Google Scholar
  28. Lorenz, M. C. & Heitman, J. Regulators of pseudohyphal differentiation in Saccharomyces cerevisiae identified through multicopy suppressor analysis in ammonium permease mutant strains. Genetics 150, 1443–1457 (1998)
    CAS PubMed PubMed Central Google Scholar
  29. Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999)
    CAS Google Scholar
  30. Gu, Z. et al. Role of duplicate genes in genetic robustness against null mutations. Nature 421, 63–66 (2003)
    ADS CAS PubMed Google Scholar
  31. Sharp, P. M. & Li, W. H. The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281–1295 (1987)
    ADS CAS PubMed PubMed Central Google Scholar
  32. Sarthy, A. V. et al. Identification and kinetic analysis of a functional homolog of elongation factor 3, YEF3 in Saccharomyces cerevisiae. Yeast 14, 239–253 (1998)
    CAS PubMed Google Scholar
  33. Boles, E. et al. Characterization of a glucose-repressed pyruvate kinase (Pyk2p) in Saccharomyces cerevisiae that is catalytically insensitive to fructose-1,6-bisphosphate. J. Bacteriol. 179, 2987–2993 (1997)
    CAS PubMed PubMed Central Google Scholar
  34. Hughes, M. K. & Hughes, A. L. Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol. 10, 1360–1369 (1993)
    CAS PubMed Google Scholar
  35. Gallardo, M. H., Bickham, J. W., Honeycutt, R. L., Ojeda, R. A. & Kohler, N. Discovery of tetraploidy in a mammal. Nature 401, 341 (1999)
    ADS CAS PubMed Google Scholar
  36. Bailey, G. S., Poulter, R. T. & Stockwell, P. A. Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. Proc. Natl Acad. Sci. USA 75, 5575–5579 (1978)
    ADS CAS PubMed PubMed Central Google Scholar
  37. Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000)
    CAS PubMed Google Scholar
  38. Blanc, G., Barakat, A., Guyot, R., Cooke, R. & Delseny, M. Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12, 1093–1101 (2000)
    CAS PubMed PubMed Central Google Scholar
  39. Sidow, A. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6, 715–722 (1996)
    CAS PubMed Google Scholar
  40. Pebusque, M. J., Coulier, F., Birnbaum, D. & Pontarotti, P. Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol. Biol. Evol. 15, 1145–1159 (1998)
    CAS PubMed Google Scholar
  41. Batzoglou, S. et al. ARACHNE: a whole-genome shotgun assembler. Genome Res. 12, 177–189 (2002)
    CAS PubMed PubMed Central Google Scholar
  42. Jaffe, D. B. et al. Whole-genome sequence assembly for mammalian genomes: arachne 2. Genome Res. 13, 91–96 (2003)
    CAS PubMed PubMed Central Google Scholar
  43. Kellis, M., Patterson, N., Birren, B., Berger, B. & Lander, E. S. Methods in comparative genomics: genome correspondence, gene identification, regulatory motif discovery. J. Comput. Biol. (in the press)
  44. Turner, R. J., Lovato, M. & Schimmel, P. One of two genes encoding glycyl-tRNA synthetase in Saccharomyces cerevisiae provides mitochondrial and cytoplasmic functions. J. Biol. Chem. 275, 27681–27688 (2000)
    CAS PubMed Google Scholar
  45. Kurtzman, C. P. & Robnett, C. J. Phylogenetic relationships among yeasts of the ‘Saccharomyces complex’ determined from multigene sequence analyses. FEMS Yeast Res. 3, 417–432 (2003)
    CAS PubMed Google Scholar

Download references