Detection of gene duplications and block duplications in eukaryotic genomes

Journal of Structural and Functional Genomics

Volumn 3, Issue 1-4, 2003, Pages 27-34

  Li, Wen Hsiung ^a   Gu, Zhenglong ^a   Cavalcanti, Andre R O ^a,b   Nekrutenko, Anton ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b FEDERAL UNIVERSITY OF PERNAMBUCO   (Brazil)

Author keywords

Codon usage bias; Database cleaning; Gene duplication rate; Gene families

Indexed keywords

CAENORHABDITIS ELEGANS; CHROMOSOME; DROSOPHILA MELANOGASTER; EUKARYOTE; GENE DUPLICATION; GENE SEQUENCE; GENOME; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA SPLICING; TECHNIQUE; YEAST;

ANIMALS; CAENORHABDITIS ELEGANS; DROSOPHILA; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME; SEQUENCE ANALYSIS, DNA; YEASTS;

CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTA; MELANOGASTER;

EID: 0037269875     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1022644628861     Document Type: Review

References (21)

1. Brosius, J. (1999) Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica, 107, 209-238.
2. Cavalcanti, A., Ferreira, R., Gu, Z. and Li W-H (2002) Patterns of gene duplication in yeast and C. elegans. J. Mol. Evol., in press.
3. Doolittle, R.F. (1995) The multiplicity of domains in proteins. Annu. Rev. Biochem., 64, 287-314.
4. Friedman, R. and Hughes, A.L. (2001) Gene duplication and the structure of eukaryotic genomes. Genome Res., 11, 373-381.
5. Gu, Z., Cavalcanti, A., Chen, F.C., Bouman, P. and Li, W.-H. (2002) Extent of gene duplication in the genomes of Drosophila, nematode and yeast. Mol. Biol. Evol., 19, 250-262.
6. Gu, Z., Wang, H., Nekrutenko, A. and Li, W.H. (2000) Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence. Gene, 259, 81-88.
7. Li, W.-H. (1997) Molecular Evolution. Sinauer Associates, Sunderland, MA.
8. Li, W.H., Gu, Z., Wang, H. and Nekrutenko, A. (2001) Evolutionary analyses of the human genome. Nature, 409, 847-849.
9. Lynch, M. and Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
10. Makalowski, W. (2000) Genomic scrap yard: how genomes utilize all that junk. Gene, 259, 61-67.
11. Nekrutenko, A. and Li, W.-H. (2001) Transposable elements are found in a large number of human protein-coding genes. Trends Genet., 17, 619-621
12. Ohno, S. (1970) Evolution by Gene Duplication, Springer-Verlag, Berlin, Germany.
13. Ponting, C.P., Schultz, J., Copley, R.R., Andrade, M.A. and Bork, P. (2000) Evolution of domain families. Adv. Protein Chem., 54, 185-244.
14. Robertson, H.M. (1998) Two large families of chemoreceptor genes in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal extensive gene duplication, diversification, movement, and intron loss. Genome Res., 8, 449-463.
15. Rost, B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
16. Rubin, G.M., Yandell, M.D., Wortman, J.R., Gabor Miklos, G.L., Nelson, C.R., Hariharan, I.K., Fortini, M.E, Li, P.W., Apweiler, R., Fleischmann, W., Cherry, J.M., Henikoff, S., Skupski, M.P., Misra, S., Ashburner, M., Birney, E., Boguski, M.S., Brody, T., Brokstein, P., Celniker, S.E., Chervitz, S.A., Coates, D., Cravchik, A., Gabrielian, A., Galle, R.E, Gelbart, W.M., George, R.A., Goldstein, L.S., Gong, F., Guan, P., Harris, N.L., Hay, B.A., Hoskins. R.A., Li, J., Li, Z., Hynes, R.O., Jones, S.J., Kuehl, P.M., Lemaitre, B., Littleton, J.T., Morrison, D.K., Mungall, C., O'Farrell, P.H., Pickeral, O.K., Shue, C., Vosshall, L.B., Zhang, J., Zhao, Q., Zheng, X.H. and Lewis. S. (2000) Comparative genomics of the eukaryotes. Science, 287, 2204-2215.
17. Seoighe, C. and Wolfe, K.H (1999) Updated map of duplicated regions in the yeast genome. Gene, 238, 253-261.
18. Tijet, N., Helvig, C. and Feyereisen, R. (2001) The cytochrome P450 gene superfamily in Drosophila melanogaster: annotation, intron-exon organization and phylogeny. Gene, 262, 189-198.
19. Viswanathan, M., Muthukumar, G., Cong, Y.S. and Lenard, J. (1994) Seripauperins of Saccharomyces cerevisiae: a new multigene family encoding serine-poor relatives of serine-rich proteins. Gene, 148, 149-153.
20. Wolfe, K.H. and Shields, D.C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387, 708-713.
21. Yamada, M., Hayatsu, N., Matsuura, A. and Ishikawa, F. (1998) Y'-Helpl, a DNA helicase encoded by the yeast subtelomeric Y' element, is induced in survivors defective for telomerase. J. Biol. Chem., 273, 33360-33366.