Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

Nature

Volumn 428, Issue 6983, 2004, Pages 617-624

  Kellis, Manolis ^a,b   Birren, Bruce W ^a   Lander, Eric S ^a,c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER AIDED ANALYSIS; FUNCTIONS; GENES; MAPPING; MATHEMATICAL MODELS; YEAST;

EVOLUTIONARY ANALYSIS; GENOME DUPLICATION; GENOME SEQUENCE;

BIODIVERSITY;

GENOME;

ARTICLE; CHROMOSOME PAIRING; CHROMOSOME STRUCTURE; CODON USAGE; FUNGAL GENETICS; GENE CONVERSION; GENE DUPLICATION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOSS; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE GENETICS; SACCHAROMYCES CEREVISIAE; SPECIES; YEAST;

CODON; EVOLUTION, MOLECULAR; GENE CONVERSION; GENE DUPLICATION; GENES, FUNGAL; GENOME, FUNGAL; MODELS, GENETIC; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SYNTENY;

FUNGI; KLUYVEROMYCES; KLUYVEROMYCES WALTII; MYXOGASTRIA; PROKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 1942452749     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02424     Document Type: Article

References (45)

1. Ohno, S. Evolution by Gene Duplication (Allen and Unwin, London, 1970).
2. Mayer, V. W. & Aguilera, A. High levels of chromosome instability in polyploids of Saccharomyces cerevisiae. Mutat. Res. 231, 177-186 (1990).
3. Wolfe, K. H. & Shields, D. C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713 (1997).
4. Seoighe, C. & Wolfe, K. H. Updated map of duplicated regions in the yeast genome. Gene 238, 253-261 (1999).
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).
6. Goffeau, A. et al. Life with 6000 genes. Science 274, 546, 563-567 (1996).
7. Philippsen, P. et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications. Nature 387, 93-98 (1997).
8. Mewes, H. W. et al. Overview of the yeast genome. Nature 387, 7-65 (1997).
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).
10. Friedman, R. & Hughes, A. L. Gene duplication and the structure of eukaryotic genomes. Genome Res. 11, 373-381 (2001).
11. Hughes, T. R. et al. Widespread aneuploidy revealed by DNA microarray expression profiling. Nature Genet. 25, 333-337 (2000).
12. Piskur, J. Origin of the duplicated regions in the yeast genomes. Trends Genet. 17, 302-303 (2001).
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).
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).
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).
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).
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).
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).
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).
20. Lynch, M. & Force, A. The probability of duplicate gene preservation by subfunctionalization. Genetics 154, 459-473 (2000).
21. Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545 (1999).
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).
24. Bell, S. P., Kobayashi, R. & Stillman, B. Yeast origin recognition complex functions in transcription silencing and DNA replication. Science 262, 1844-1849 (1993).
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).
26. Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686-691 (2003).
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).
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).
29. Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
30. Gu, Z. et al. Role of duplicate genes in genetic robustness against null mutations. Nature 421, 63-66 (2003).
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).
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).
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).
34. Hughes, M. K. & Hughes, A. L. Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol. 10, 1360-1369 (1993).
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).
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).
37. Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401-437 (2000).
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).
39. Sidow, A. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6, 715-722 (1996).
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).
41. Batzoglou, S. et al. ARACHNE: a whole-genome shotgun assembler. Genome Res. 12, 177-189 (2002).
42. Jaffe, D. B. et al. Whole-genome sequence assembly for mammalian genomes: arachne 2. Genome Res. 13, 91-96 (2003).
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).
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).