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.
Figures
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
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
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
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.
Similar articles
- Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates.
Bu L, Bergthorsson U, Katju V. Bu L, et al. BMC Evol Biol. 2011 Sep 28;11:279. doi: 10.1186/1471-2148-11-279. BMC Evol Biol. 2011. PMID: 21955875 Free PMC article. - Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae.
Kim SH, Yi SV. Kim SH, et al. Mol Biol Evol. 2006 May;23(5):1068-75. doi: 10.1093/molbev/msj115. Epub 2006 Mar 1. Mol Biol Evol. 2006. PMID: 16510556 - Divergence in the spatial pattern of gene expression between human duplicate genes.
Makova KD, Li WH. Makova KD, et al. Genome Res. 2003 Jul;13(7):1638-45. doi: 10.1101/gr.1133803. Genome Res. 2003. PMID: 12840042 Free PMC article. - Retention of protein complex membership by ancient duplicated gene products in budding yeast.
Musso G, Zhang Z, Emili A. Musso G, et al. Trends Genet. 2007 Jun;23(6):266-9. doi: 10.1016/j.tig.2007.03.012. Epub 2007 Apr 10. Trends Genet. 2007. PMID: 17428571 Review. - Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico.
Raes J, Van de Peer Y. Raes J, et al. Appl Bioinformatics. 2003;2(2):91-101. Appl Bioinformatics. 2003. PMID: 15130825 Review.
Cited by
- The evolution of tenascins.
Adams JC, Tucker RP. Adams JC, et al. BMC Ecol Evol. 2024 Sep 14;24(1):121. doi: 10.1186/s12862-024-02306-2. BMC Ecol Evol. 2024. PMID: 39277743 Free PMC article. - Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms.
Shi T, Gao Z, Chen J, Van de Peer Y. Shi T, et al. Plant Cell. 2024 Oct 3;36(10):4323-4337. doi: 10.1093/plcell/koae227. Plant Cell. 2024. PMID: 39121058 - Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins.
Dani R, Pawloski W, Chaurasiya DK, Srilatha NS, Agarwal S, Fushman D, Naganathan AN. Dani R, et al. Biochemistry. 2023 Oct 17;62(20):2982-2996. doi: 10.1021/acs.biochem.3c00449. Epub 2023 Oct 3. Biochemistry. 2023. PMID: 37788430 - Increased mutation and gene conversion within human segmental duplications.
Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M; Human Pangenome Reference Consortium; Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE. Vollger MR, et al. Nature. 2023 May;617(7960):325-334. doi: 10.1038/s41586-023-05895-y. Epub 2023 May 10. Nature. 2023. PMID: 37165237 Free PMC article. - Evolutionary Trajectories of New Duplicated and Putative De Novo Genes.
Montañés JC, Huertas M, Messeguer X, Albà MM. Montañés JC, et al. Mol Biol Evol. 2023 May 2;40(5):msad098. doi: 10.1093/molbev/msad098. Mol Biol Evol. 2023. PMID: 37139943 Free PMC article.
References
- 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
- Bennetzen, J.L. and Hall, B.D. 1982. Codon selection in yeast. Journal of Biological Chemistry 257: 3026–3031. - PubMed
- The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012–2018. - PubMed
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Molecular Biology Databases