Detection of gene duplications and block duplications in eukaryotic genomes
Rent the article at a discountRent now
* Final gross prices may vary according to local VAT.Get Access
Several eukaryotic genomes have been completely sequenced and this provides an opportunity to investigate the extent and characteristics (e.g., single gene duplication, block duplication, etc.) of gene duplication in a genome. Detecting duplicate genes in a genome, however, is not a simple problem because of several complications such as domain shuffling, the existence of isoforms derived from alternative splicing, and annotational errors in the databases. We describe a method for overcoming these difficulties and the extents of gene duplication in the genomes of Drosophila melanogaster, Caenorhabditis elegans, and yeast inferred from this method. We also describe a method for detecting block duplications in a genome. Application of this method showed that block duplication is a common phenomenon in both yeast and nematode. The patterns of block duplication in the two species are, however, markedly different. Yeast shows much more extensive block duplication than nematode, with some chromosomes having more than 40% of the duplications derived from block duplications. Moreover, in yeast the majority of block duplications occurred between chromosomes, while in nematode most block duplications occurred within chromosomes.
- Brosius, J. (1999) Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica, 107, 209-238.
- 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.
- Doolittle, R.F. (1995) The multiplicity of domains in proteins.Annu. Rev. Biochem., 64, 287-314.
- Friedman, R. and Hughes, A.L. (2001) Gene duplication and the structure of eukaryotic genomes. Genome Res., 11, 373-381.
- 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.
- 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.
- Li, W.-H. (1997) Molecular Evolution. Sinauer Associates, Sunderland, MA.
- Li, W.H., Gu, Z., Wang, H. and Nekrutenko, A. (2001) Evolutionary analyses of the human genome. Nature, 409, 847-849.
- Lynch, M. and Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
- Makalowski, W. (2000) Genomic scrap yard: how genomes utilize all that junk. Gene, 259, 61-67.
- 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
- Ohno, S. (1970) Evolution by Gene Duplication, Springer-Verlag, Berlin, Germany.
- 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.
- 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.
- Rost, B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
- 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.F., 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.
- Seoighe, C. and Wolfe, K.H (1999) Updated map of duplicated regions in the yeast genome. Gene, 238, 253-261.
- 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.
- 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.
- Wolfe, K.H. and Shields, D.C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387, 708-713.
- Yamada, M., Hayatsu, N., Matsuura, A. and Ishikawa, F. (1998) Y'-Help1, a DNA helicase encoded by the yeast subtelomeric Y' element, is induced in survivors defective for telomerase. J. Biol. Chem., 273, 33360-33366.
- Detection of gene duplications and block duplications in eukaryotic genomes
Journal of Structural and Functional Genomics
Volume 3, Issue 1-4 , pp 27-34
- Cover Date
- Print ISSN
- Online ISSN
- Kluwer Academic Publishers
- Additional Links
- codon usage bias
- database cleaning
- gene duplication rate
- gene families
- Author Affiliations
- 1. Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA
- 2. Departamento de Quimica Fundamental, Universidade Federal de Pernambuco, Brazil