Paleogenomics or the search for remnant duplicated copies of the yeast DUP240 gene family in intergenic areas

Molecular Biology and Evolution

Volumn 22, Issue 9, 2005, Pages 1764-1771

  Wirth, Bénédicte ^a   Louis, Véronique Leh ^a   Potier, Serge ^a   Souciet, Jean Luc ^a   Despons, Laurence ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

DUP240 family; Fate of duplicated genes; Gene death; Pseudogenes; Relics; Saccharomyces cerevisiae

Indexed keywords

SPACER DNA;

ARTICLE; CHROMOSOME REARRANGEMENT; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DEGENERATION; DNA FLANKING REGION; GENE DELETION; GENE DUPLICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYSIS; GENOME; GENOMICS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; ORTHOLOGY; PALEONTOLOGY; PARALOGY; PROTEIN MOTIF; SACCHAROMYCES CEREVISIAE; SPECIES COMPARISON; YEAST;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, FUNGAL; HISTORY, ANCIENT; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; OPEN READING FRAMES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ANALYSIS, DNA; TANDEM REPEAT SEQUENCES;

SACCHAROMYCES CEREVISIAE;

EID: 23944515058     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi170     Document Type: Article

References (27)

1. Blake, R. D., S. T. Hess, and J. Nicholson-Tuell. 1992. The influence of nearest neighbors on the rate and pattern of spontaneous point mutations. J. Mol. Evol. 34:189-200.
2. Blanchard, J. L., and G. W. Schmidt. 1996. Mitochondrial DNA migration events in yeast and humans: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns. Mol. Biol. Evol. 13:537-548.
3. Cliften, P., P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, and M. Johnston. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76.
4. Cole, S. T., K. Eiglmeier, J. Parkhill et al. (44 co-authors). 2001. Massive gene decay in the leprosy bacillus. Nature 409:1007-1011.
5. Farabaugh, P. J., and G. R. Fink. 1980. Insertion of the eukaryotic transposable element Ty1 creates a 5-base pair duplication. Nature 286:352-356.
6. Feuermann, M., J. de Montigny, S. Potier, and J. L. Souciet. 1997. The characterization of two new clusters of duplicated genes suggests a 'Lego' organization of the yeast Saccharomyces cerevisiae chromosomes. Yeast 13:861-869.
7. Fischer, G., C. Neuveglise, P. Durrens, C. Gaillardin, and B. Dujon. 2001. Evolution of gene order in the genomes of two related yeast species. Genome Res. 11:2009-2019.
8. Gafner, J., and P. Philippsen. 1980. The yeast transposon Ty1 generates duplications of target DNA on insertion. Nature 286:414-418.
9. Goffeau, A., R. Aert, M. L. Agostini-Carbone, A. Ahmed, M. Aigle, and L. Alberghina. 1997. The yeast genome directory. Nature 387(Suppl.):5-105.
10. Harrison, P. M., H. Hegyi, S. Balasubramanian, N. M. Luscombe, P. Bertone, N. Echols, T. Johnson, and M. Gerstein. 2002. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res. 12:272-280.
11. Homma, K., S. Fukuchi, T. Kawabata, M. Ota, and K. Nishikawa. 2002. A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome. Gene 294:25-33.
12. Kellis, M., N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254.
13. Lafontaine, I., G. Fischer, E. Talla, and B. Dujon. 2004. Gene relics in the genome of the yeast Saccharomyces cerevisiae. Gene 335:1-17.
14. Leh-Louis, V., B. Wirth, L. Despons, S. Wain-Hobson, S. Potier, and J. L. Souciet. 2004a. Differential evolution of the Saccharomyces cerevisiae DUP240 paralogs and implication of recombination in phylogeny. Nucleic Acids Res. 32:2069-2078.
15. Leh-Louis, V., B. Wirth, S. Potier, J. L. Souciet, and L. Despons. 2004b. Expansion and contraction of the DUP240 multigene family in Saccharomyces cerevisiae populations. Genetics 167:1611-1619.
16. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
17. Massingham, T., L. J. Davies, and P. Lio. 2001. Analysing gene function after duplication. Bioessays 23:873-876.
18. Mighell, A. J., N. R. Smith, P. A. Robinson, and A. F. Markham. 2000. Vertebrate pseudogenes. FEBS Lett. 468:109-114.
19. Ophir, R., and D. Graur. 1997. Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene 205:191-202.
20. Ophir, R., T. Itoh, D. Graur, and T. Gojobori. 1999. A simple method for estimating the intensity of purifying selection in protein-coding genes. Mol. Biol. Evol. 16:49-53.
21. Poirey, R., L. Despons, V. Leh, M. J. Lafuente, S. Potier, J. L. Souciet, and J. C. Jauniaux. 2002. Functional analysis of the Saccharomyces cerevisiae DUP240 multigene family reveals membrane-associated proteins that are not essential for cell viability. Microbiology 148:2111-2123.
22. Prince, V. E., and F. B. Pickett. 2002. Splitting pairs: the diverging fates of duplicated genes. Nat. Rev. Genet. 3:827-837.
23. Ricchetti, M., C. Fairhead, and B. Dujon. 1999. Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature 402:96-100.
24. Vanin, E. F. 1985. Processed pseudogenes: characteristics and evolution. Annu. Rev. Genet. 19:253-272.
25. Yu, X., and A. Gabriel. 1999. Patching broken chromosomes with extranuclear cellular DNA. Mol. Cell 4:873-881.
26. Zhang, Z., and M. Gerstein. 2004. Large-scale analysis of pseudogenes in the human genome. Curr. Opin. Genet. Dev. 14:328-335.
27. Zhang, Z. L., P. M. Harrison, and M. Gerstein. 2002. Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes. J. Mol. Biol. 323:811-822.