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

Abstract

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 > or =I (I = 30% if L > or = 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 > or = 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 (K(S)) < 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 K(S) < 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.

The evolutionary demography of duplicate genes

“…The average rate of origin of new duplicates in this study, 0.01/gene/MY, is about the same as that reported in our earlier study. Gu et al (2002) also recently reported estimates of the rate of origin of duplicates genes in D. melanogaster, C. elegans, and S. cerevisiae. As in our study, these authors employed pre-screening devices to avoid pseudogenes, alternatively spliced variants, and annotation errors, but their additional methods of analysis deviated from those used herein in a number of ways.…”

“…As in our study, these authors employed pre-screening devices to avoid pseudogenes, alternatively spliced variants, and annotation errors, but their additional methods of analysis deviated from those used herein in a number of ways. For example, Gu et al (2002) did not make a distinction between the number of duplicate pairs and the actual (necessarily smaller) number of duplication events; they included very large multigene families, whereas we used an arbitrary cutoff for family size of five; they attempted to remove incomplete or chimeric duplicates; and they eliminated some duplicate pairs in which the nucleotide substitution levels in flanking regions exceeded those in silent sites. Despite these differences, it is comforting that estimates from both studies for B appear to deviate by no more than a factor of three.…”

“…We recently obtained indirect estimates of the rates of birth and loss of new genes through censuses of the contents of the then largely sequenced nuclear genomes of several eukaryotes (Lynch and Conery 2000), and additional estimates using somewhat different criteria have been published by Gu et al (2002). Since these studies were performed, nearly complete genomic sequences have emerged for several species and all of the pre-existing databases have been refined considerably.…”

Gene duplications, robustness and evolutionary innovations

“…They can tolerate more nucleotide changes than their single copy counterparts. The phenomenon is evident most clearly on a whole-genome scale 15,16 , where recent gene duplicates in various eukaryotes tolerate 10-fold more amino acid changes than old duplicates 15 . Eventually, the accumulating changes may cause duplicates to diversify their function, and sometimes quite rapidly 11,17,18 .…”

The regulatory code for transcriptional response diversity and its relation to genome structural properties in Arabidopsis thaliana

“…Duplicated genes within the Arabidopsis genome were identified following a method introduced by Gu and coworkers [54,55]. This method is based on an all-againstall sequence comparison of protein sequences that are not splice variants of the same gene and require at least 30% amino acid sequence identity with adjusted higher thresholds for short sequences.…”