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Comparative Study
. 2001 Mar;11(3):373-81.
doi: 10.1101/gr.155801.

Gene duplication and the structure of eukaryotic genomes

R Friedman  1 , A L Hughes
Affiliations
Comparative Study

Gene duplication and the structure of eukaryotic genomes

R Friedman et al. Genome Res. 2001 Mar.

Abstract

A simple method for understanding how gene duplication has contributed to genomic structure was applied to the complete genomes of Caenorhabditis elegans, Drosophila melanogaster, and yeast Saccharomyces cerevisiae. By this method, the genes belonging to gene families (the paranome) were identified, and the extent of sharing of two or more families between genomic windows was compared with that expected under a null model. The results showed significant evidence of duplication of genomic blocks in both C. elegans and yeast. In C. elegans, the five block duplications identified all occurred intra-chromosomally, and all but one occurred quite recently. In yeast, by contrast, 39 duplicated blocks were identified, and all but one of these was inter-chromosomal. Of these 39 blocks, 28 showed evidence of ancient duplication, possibly as a result of an ancient polyploidization event. By contrast, three blocks showed evidence of very recent duplication, while seven others showed a mixture of ancient and recent duplication events. Thus, duplication of genomic blocks has been an ongoing feature of yeast evolution over the past 200--300 million years.

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Figures

Figure 1
Figure 1
Frequency distribution of the proportion of synonymous difference per synonymous site (pS) in comparisons of 240 pairs of duplicated genes in 39 duplicated blocks in the yeast genome.
Figure 2
Figure 2
Relationship between the proportion synonymous difference per synonymous site (pS) and mean codon adaptation index (CAI) for 240 pairs of duplicated genes in 39 duplicated blocks in the yeast genome. There was a significant negative correlation (r = − 0.510; P <0.001).
Figure 3
Figure 3
Mean proportion synonymous difference per synonymous site (pS), with range indicated by vertical bars, for 208 duplicated gene pairs in 39 duplicated blocks in the yeast genome. Gene pairs with mean codon adaptation index (CAI) >0.50 were excluded.
Figure 4
Figure 4
Hypothetical evolutionary scenarios for generating (A) a genomic block containing one anciently duplicated pair of genes within a recently duplicated genomic block; and (B) a group of genes duplicated by an ancient genomic duplication plus one more recently duplicated gene pair.
See this image and copyright information in PMC

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