Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication

Genetics

Volumn 175, Issue 3, 2007, Pages 1341-1350

  Byrne, Kevin P ^a   Wolfe, Kenneth H ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANDIDA GLABRATA; CONTROLLED STUDY; FUNGAL GENE; FUNGUS; GENE DUPLICATION; GENE FUNCTION; GENE LOSS; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CASTELLII; SACCHAROMYCES CEREVISIAE;

CANDIDA GLABRATA; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DELETION; GENE DUPLICATION; GENOME, FUNGAL; PHYLOGENY; SACCHAROMYCES; SPECIES SPECIFICITY;

CANDIDA GLABRATA; KLUYVEROMYCES LACTIS; SACCHAROMYCES CEREVISIAE;

EID: 34249067353     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.066951     Document Type: Article

References (41)

1. BENJAMINI, Y., and Y. HOCKBERG, 1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57: 289-300.
2. BLANC, G., and K. H. WOLFE, 2004 Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691.
3. BYRNE, K. P., and G. BLANC, 2006 Computational analyses of ancient polyploidy. Curr. Bioinform. 1: 131-146.
4. BYRNE, K. P., and K. H.WOLFE, 2005 The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15: 1456-1461.
5. BYRNES, J. K., G. P. MORRIS and W. H. LI, 2006 Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion. Mol. Biol. Evol. 23: 1136-1143.
6. CHENNA, R., H. SUGAWARA, T. KOIKE, R. LOPEZ, T. J. GIBSON et al., 2003 Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31: 3497-3500.
7. CHRISTIE, K. R., S. WENG, R. BALAKRISHNAN, M. C. COSTANZO, K. DOLINSKI et al., 2004 Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 32: D311-D314.
8. CLIFTEN, P., P. SUDARSANAM, A. DESIKAN, L. FULTON, B. FULTON et al., 2003 Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
9. CLIFTEN, P. F., R. S. FULTON, R. K. WILSON and M. JOHNSTON, 2006 After the duplication: gene loss and adaptation in Saccharomyces genomes. Genetics 172: 863-872.
10. CONANT, G. C., and A. WAGNER, 2003 Asymmetric sequence divergence of duplicate genes. Genome Res. 13: 2052-2058.
11. DIETRICH, F. S., S. VOEGELI, S. BRACHAT, A. LERCH, K. GATES et al., 2004 The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304: 304-307.
12. DUJON, B., D. SHERMAN, G. FISCHER, P. DURRENS, S. CASAREGOLA et al., 2004 Genome evolution in yeasts. Nature 430: 35-44.
13. FARES, M. A., K. P. BYRNE and K. H. WOLFE, 2006 Rate asymmetry after genome duplication causes substantial long branch attraction artifacts in the phylogeny of Saccharomyces species. Mol. Biol. Evol. 23: 245-253.
14. FORCE, A., M. LYNCH, F. B. PICKETT, A. AMORES, Y. L. YAN et al., 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
15. FREDERICK, D. L., and K. TATCHELL, 1996 The REG2 gene of Saccharomyces cerevisiae encodes a type 1 protein phosphatase-binding protein that functions with Reg1p and the Snf1 protein kinase to regulate growth. Mol. Cell. Biol. 16: 2922-2931.
16. GOFFEAU, A., B. G. BARRELL, H. BUSSEY, R.W. DAVIS, B. DUJON et al., 1996 Life with 6000 genes. Science 274: 546, 563-567.
17. GULDENER, U., M. MUNSTERKOTTER, G. K ASTENMULLER, N. STRACK, J. VAN HELDEN et al., 2005 CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res. 33: D364-D368.
18. HE, X., and J. ZHANG, 2005 Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169: 1157-1164.
19. JIANG, H., K. TATCHELL, S. LIU and C. A. MICHELS, 2000 Protein phosphatase type-1 regulatory subunits Reg1p and Reg2p act as signal transducers in the glucose-induced inactivation of maltose permease in Saccharomyces cerevisiae. Mol. Gen. Genet. 263: 411-422.
20. KANIAK, A., Z. XUE, D. MACOOL, J. H. KIM and M. JOHNSTON, 2004 Regulatory network connecting two glucose signal transduction pathways in Saccharomyces cerevisiae. Eukaryot. Cell 3: 221-231.
21. KELLIS, M., B. W. BIRREN and E. S. LANDER, 2004 Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
22. KRAKAUER, D. C., and M. A. NOWAK, 1999 Evolutionary preservation of redundant duplicated genes. Semin. Cell Dev. Biol. 10: 555-559.
23. LI, W. H., 1997 Molecular Evolution. Sinauer Associates, Sunderland, MA.
24. LYNCH, M., and A. FORCE, 2000a The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
25. LYNCH, M., and A. G. FORCE, 2000b The origin of interspecies genomic incompatibility via gene duplication. Am. Nat. 156: 590-605.
26. LYNCH, M., and V. KATJU, 2004 The altered evolutionary trajectories of gene duplicates. Trends Genet. 20: 544-549.
27. MAERE, S., S. DE BODT, J. RAES, T. CASNEUF, M. VAN MONTAGU et al., 2005 Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. USA 102: 5454-5459.
28. OHNO, S., 1970 Evolution by Gene Duplication. George Allen & Unwin, London.
29. PAPP, B., C. PAL and L. D. HURST, 2003 Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
30. PATERSON, A. H., B. A. CHAPMAN, J. C. KISSINGER, J. E. BOWERS, F. A. FELTUS et al., 2006 Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet. 22: 597-602.
31. PHILLIPS, M. J., F. DELSUC and D. PENNY, 2004 Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21: 1455-1458.
32. SCANNELL, D. R., K. P. BYRNE, J. L. GORDON, S. WONG and K. H. WOLFE, 2006 Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440: 341-345.
33. SUGINO, R. P., and H. INNAN, 2006 Selection for more of the same product as a force to enhance concerted evolution of duplicated genes. Trends Genet. 22: 642-644.
34. SWOFFORD, D. L., 2003 PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, MA.
35. TER LINDE, J. J., and H. Y. STEENSMA, 2002 A microarray-assisted screen for potential Hap1 and Rox1 target genes in Saccharomyces cerevisiae. Yeast 19: 825-840.
36. VAN DE PEER, Y., J. S. TAYLOR, I. BRAASCH and A. MEYER, 2001 The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J. Mol. Evol. 53: 436-446.
37. VAN HOOF, A., 2005 Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication. Genetics 171: 1455-1461.
38. WOLFE, K., 2000 Robustness - it's not where you think it is. Nat. Genet. 25: 3-4.
39. WOLFE, K. H., and D. C. SHIELDS, 1997 Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
40. YANG, Z., 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
41. ZHANG, L., T. J. VISION and B. S. GAUT, 2002 Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol. Biol. Evol. 19: 1464-1473.