Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

Briefings in Bioinformatics

Volumn 12, Issue 5, 2011, Pages 442-448

  Huerta cepas, Jaime ^a   Dopazo, Joaquín ^b   Huynen, Martijn A ^c   Gabaldón, Toni ^d  

^a Comparative Genomics Group at CRG ^*  (Spain)

^b CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d Genomics program in the CRG ^*  (Spain)

Author keywords

Functional divergence; Gene duplication; Orthology; Paralogy; Tissue expression

Indexed keywords

ANIMAL; ANTIBODY SPECIFICITY; ARTICLE; GENE DUPLICATION; GENE EXPRESSION; GENOME; HUMAN; MOLECULAR EVOLUTION; MOUSE; NUCLEOTIDE SEQUENCE;

ANIMALS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION; GENOME; HUMANS; MICE; ORGAN SPECIFICITY;

MAMMALIA; VERTEBRATA;

EID: 80053194329     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbr022     Document Type: Article

References (32)

1. Ohno SS. Evolution by gene duplication. New York: Springer, 1970.
2. Force A, Lynch M, Pickett FB, et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999;151:1531-45.
3. Lynch M, Force A. The probability of duplicate gene preservation by subfunctionalization. Genetics 2000;154:459-73.
4. Innan H, Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11:97-108.
5. Freilich S, Massingham T, Blanc E, et al. Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins. Genome Biol 2006;7:R89.
6. Huminiecki L, Wolfe KH. Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res 2004;14:1870-9.
7. Gu Z, Rifkin SA, White KP, et al. Duplicate genes increase gene expression diversity within and between species. Nat Genet 2004;36:577-9.
8. Ha M, Kim ED, Chen ZJ. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci USA 2009;106:2295-300.
9. Farre D, Alba MM. Heterogeneous patterns of gene expression diversification in mammalian gene duplicates. Mol Biol Evol 2010;27:325-35.
10. Milinkovitch MC, Helaers R, Tzika AC. Historical constraints on vertebrate genome evolution. Genome Biol Evol 2010;2010:13-18.
11. Gu Z, Nicolae D, Lu HH-S, et al. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet: TIG 2002;18:609-13.
12. Makova KD, Li W-H. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res 2003;13:1638-45.
13. Ganko EW, Meyers BC, Vision TJ. Divergence in Expression between Duplicated Genes in Arabidopsis. Mol Biol Evol 2007;24:2298-309.
14. Haberer G, Hindemitt T, Meyers BC, et al. Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol 2004;136: 3009-22.
15. Wagner A. Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol 2002;19:1760-8.
16. Tirosh I, Barkai N. Evolution of gene sequence and gene expression are not correlated in yeast. Trends Genet 2008;24: 109-13.
17. Gao LZ, Innan H. Very low gene duplication rate in the yeast genome. Science 2004;306:1367-70.
18. Huerta-Cepas J, Gabaldón T. Assigning duplication events to relative temporal scales in genome-wide studies. Bioinformatics 2011;27:38-45.
19. Studer RA, Robinson-Rechavi M. How confident can we be that orthologs are similar, but paralogs differ? Trends Genet 2009;25:210-16.
20. Jordan IK, Mario-Ramírez L, Koonin EV. Evolutionary significance of gene expression divergence. Gene 2005; 345:119-26.
21. Yanai I, Graur D, Ophir R. Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS 2004;8:15-24.
22. Zou C, Lehti-Shiu MD, Thomashow M, et al. Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana. PLoS Genet 2009;5:e1000581.
23. Tirosh I, Barkai N. Comparative analysis indicates regulatory neofunctionalization of yeast duplicates. Genome Biol 2007;8:R50.
24. Chung WY, Albert R, Albert I, et al. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC Bioinformatics 2006;7:46.
25. Casneuf T, De Bodt S, Raes J, etal. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol 2006;7:R13.
26. Huerta-Cepas J, Dopazo H, Dopazo J, et al. The human phylome. Genome Biol 2007;8:R109.
27. Su AI, Wiltshire T, Batalov S, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004;101:6062-7.
28. Bastian F, Parmentier G, Roux J, etal. Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. Data Integration Life Sci 2008;5109:124-31.
29. Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, et al. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res 2011;39: D556-60.
30. Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 2010;11:24.
31. Pereira V, Waxman D, Eyre-Walker A. A problem with the correlation coefficient as a measure of gene expression divergence. Genetics 2009;183:1597-600.
32. Van de Peer Y, Fawcett JA, Proost S, et al. The flowering world: a tale of duplications. Trends Plant Sci 2009;14:680-8.