Asymmetric sequence divergence of duplicate genes - PubMed (original) (raw)

Comparative Study

Asymmetric sequence divergence of duplicate genes

Gavin C Conant et al. Genome Res. 2003 Sep.

Abstract

Much like humans, gene duplicates may be created equal, but they do not stay that way for long. For four completely sequenced genomes we show that 20%-30% of duplicate gene pairs show asymmetric evolution in the amino acid sequence of their protein products. That is, one of the duplicates evolves much faster than the other. The greater this asymmetry, the greater the ratio Ka/Ks of amino acid substitutions (Ka) to silent substitutions (Ks) in a gene pair. This indicates that most asymmetric divergence may be caused by relaxed selective constraints on one of the duplicates. However, we also find some candidate duplicates where positive (directional) selection of beneficial mutations (Ka/Ks > 1) may play a role in asymmetric divergence. Our analysis rests on a codon-based model of molecular evolution that allows a test for asymmetric divergence in Ka. The method is also more sensitive in detecting positive selection (Ka/Ks > 1) than models relying only on pairwise gene comparisons.

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Figures

Figure 1

Figure 1

Schematic representation of our model tree. Two duplicates are presumed to have diverged from an outgroup gene. Each of the three branches of this tree is allowed to have its own Ks and Ka values.

Figure 2

Figure 2

Significance of observed differences in Ka. On the X-axis is plotted the absolute value of the difference in Ka value between two duplicates. The Y-axis gives the negative logarithm (to base 10) of the P value for that pair. (A) All asymmetric duplicate pairs shown. (B) Only the square region marked in panel A is shown. The dashed line in B shows the significance level of P = 0.05.

Figure 3

Figure 3

Correlation of the normalized difference in Ka between two duplicates and the difference in the selective constraint for those two duplicates. The variables on the axes labels are |Δ_Ka_| = |(_Ka_1 – _Ka_2)/(_Ka_1 + Ka_2)| and |Δ_Ka/Ks| = |(_Ka_1/_Ks_1 – _Ka_2/_Ks_2)/(_Ka_1/_Ks_1 + _Ka_2/_Ks_2)|, respectively. (A) S. cerevisiae. (B) D. melanogaster. (C) C. elegans.

Figure 4

Figure 4

Triplet-based analysis is more sensitive in detecting positive selection. Number of cases where at least one duplicate in a pair has Ka/Ks > 1.0 for the four organisms shown using our triplet method (black) and using the conventional pairwise estimation (grey). The total number of duplicates pairs for which we determined Ka/Ks in this analysis was 22 for S. cerevisiae, 14 for S. pombe, 44 for D. melanogaster, and 164 for C. elegans.

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References

    1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F. et. al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185–2195. - PubMed
    1. Bennetzen, J.L. and Hall, B.D. 1982. Codon selection in yeast. Journal of Biological Chemistry 257: 3026–3031. - PubMed
    1. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012–2018. - PubMed
    1. Cherry, J.M., Adler, C., Ball, C., Chervitz, S.A., Dwight, S.S., Hester, E.T., Jia, Y., Juvik, G., Roe, T., Schroeder, M. et al. 1998. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26: 73–80. - PMC - PubMed
    1. Conant, G.C. and Wagner, A. 2002. GenomeHistory: A software tool and its application to fully sequenced genomes. Nucleic Acids Res. 30: 3378–3386. - PMC - PubMed

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