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Molecular Biology and Evolution 19:256-262 (2002)
© 2002 Society for Molecular Biology and Evolution

Extent of Gene Duplication in the Genomes of Drosophila, Nematode, and Yeast

Zhenglong Gu, Andre Cavalcanti, Feng-Chi Chen, Peter Bouman and Wen-Hsiung Li

*Department of Ecology and Evolution
{dagger}Department of Statistics, University of Chicago

We conducted a detailed analysis of duplicate genes in three complete genomes: yeast, Drosophila, and Caenorhabditis elegans. For two proteins belonging to the same family we used the criteria: (1) their similarity is >=I (I = 30% if L >= 150 a.a. and I = 0.01n + 4.8L-0.32(1 + exp(-L/1000)) if L < 150 a.a., where n = 6 and L is the length of the alignable region), and (2) the length of the alignable region between the two sequences is >=80% of the longer protein. We found it very important to delete isoforms (caused by alternative splicing), same genes with different names, and proteins derived from repetitive elements. We estimated that there were 530, 674, and 1,219 protein families in yeast, Drosophila, and C. elegans, respectively, so, as expected, yeast has the smallest number of duplicate genes. However, for the duplicate pairs with the number of substitutions per synonymous site (KS) < 0.01, Drosophila has only seven pairs, whereas yeast has 58 pairs and nematode has 153 pairs. After considering the possible effects of codon usage bias and gene conversion, these numbers became 6, 55, and 147, respectively. Thus, Drosophila appears to have much fewer young duplicate genes than do yeast and nematode. The larger numbers of duplicate pairs with KS < 0.01 in yeast and C. elegans were probably largely caused by block duplications. At any rate, it is clear that the genome of Drosophila melanogaster has undergone few gene duplications in the recent past and has much fewer gene families than C. elegans.


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