Detection of gene duplications and block duplications in eukaryotic genomes.
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.
Li
Wen-Hsiung
WH
Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. whli@uchicago.edu
Gu
Zhenglong
Z
Cavalcanti
Andre R O
AR
Nekrutenko
Anton
A
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D004330:Drosophila / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D016678:Genome; D017422:Sequence Analysis, DNA; D015003:Yeasts / Q000235:genetics