Paralogs in polyploids: One for all and all for one?

Plant Cell

Volumn 17, Issue 1, 2005, Pages 4-11

  Veitia, Reiner A ^a  

^a UNIVERSITÉ PARIS DESCARTES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GENE; GENE DOSAGE; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENETICS; GENOME; MUTATION; PLANT; POLYPLOIDY; REGULATOR GENE; REVIEW;

GENE DOSAGE; GENE DUPLICATION; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENES, REGULATOR; GENOME, PLANT; MUTATION; PLANTS; POLYPLOIDY;

EID: 23044465906     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.104.170130     Document Type: Review

References (40)

1. Adams, K.L., Cronn, R., Percifield, R., and Wendel, J.F. (2003). Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA 100, 4649-4654.
2. Ahn, S., and Tanksley, S.D. (1993). Comparative linkage maps of the rice and maize genomes. Proc. Natl. Acad. Sci. USA 90, 7980-7984.
3. Bennett, M.D. (1972). Nuclear DNA content and minimum generation time in herbaceous plants. Proc. R. Soc. Lond. B Biol. Sci. 181, 109-135.
4. Birchler, J.A., Bhadra, U., Bhadra, M.P., and Auger, D.L. (2001). Dosage-dependent gene regulation in multicellular eukaryotes: Implications for dosage compensation, aneuploid syndromes, and quantitative traits. Dev. Biol. 234, 275-288.
5. Blanc, G., and Wolfe, K.H. (2004). Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16, 1679-1691.
6. Bowers, J.E., Chapman, B.A., Rong, J., and Paterson, A.M. (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433-438.
7. Cavalier-Smith, T. (1982). Skeletal DNA and the evolution of genome size. Annu. Rev. Biophys. Bioeng. 11, 273-302.
8. Chen, Z.J., Comai, L., and Pikaard, C.S. (1998). Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc. Natl. Acad. Sci. USA 95, 14891-14896.
9. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., and Postlethwait, J. (1999). Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545.
10. Gibson, T.J., and Spring, J. (1998). Genetic redundancy in vertebrates: Polyploidy and persistance of genes encoding multidomain proteins. Trends Genet. 14, 46-49.
11. Gregory, T.R. (2001). Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol. Rev. Camb. Philos. Soc. 76, 65-101.
12. Gu, Z., Steinmetz, L.M., Gu, X., Scharfe, C., Davis, R.W., and Li, W.H. (2003). Role of duplicate genes in genetic robustness against null mutations. Nature 421, 63-66.
13. Guo, M., Davis, D., and Birchler, U.A. (1996). Dosage effects on gene expression in a maize ploidy series. Genetics 142, 1349-1355.
14. Haberer, G., Hindemitt, T., Meyers, B.C., and Mayer, K.F. (2004). Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol. 136, 3009-3022.
15. Hodgkin, J. (2000). A view of mount Drosophila. Nature 404, 442-443.
16. Hughes, M.K., and Hughes, A.L (1993). Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol. 10, 1360-1369.
17. Huminiecki, L., and Wolfe, K.H. (2004). Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res. 14, 1870-1879.
18. Kellis, M., Birren, B.W., and Lander, E.S. (2004). Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428, 617-624.
19. Kellogg, E.A. (2003). What happens to genes in duplicated genomes. Proc. Natl. Acad. Sci. USA 100, 4369-4371.
20. Kondrashov, F.A., and Koonin, E.V. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet. 20, 287-290.
21. Lemos, B., Meiklejohn, C.D., and Hartl, D.L. (2004). Regulatory evolution across the protein interaction network. Nat. Genet. 36, 1059-1060.
22. Lynch, M., and Conery, U.S. (2000). The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155.
23. Makalowski, W. (2001). Are we polyploids? A brief history of one hypothesis. Genome Res. 11, 667-670.
24. Masterson, J. (1994). Stomatal size in fossil plants: Evidence for polyploidy in majority of angiosperms. Science 264, 421-423.
25. Ohno, S. (1970). Evolution by Gene Duplication. (London: George Allen and Unwin).
26. Otto, S.P., and Whitton, J. (2000). Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401-437.
27. Orr, H.A., and Otto, S.P. (1994). Does diploidy increase the rate of adaptation? Genetics 136, 1475-1480.
28. Ozkan, H., Levy, A.A., and Feldman, M. (2001) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13, 1735-1747.
29. Papp, B., Pal, C., and Hurst, L.D. (2003). Dosage sensitivity and the evolution of gene families in yeast. Nature 424, 194-197.
30. Pikaard, C.S. (2000). The epigenetics of nucleolar dominance. Trends Genet. 16, 495-500.
31. Pires, U.C., Zhao, J.W., Schranz, M.E., Leon, E.J., Quijada, P.A., Lukens, L.N., and Osborn, T.C. (2004). Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol. J. Linnean Soc. Lond. 82, 675-688.
32. Seoighe, C., and Gehring, C. (2004). Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet. 20, 461-464.
33. Veitia, R.A. (2002). Exploring the etiology of haploinsufficiency. Bioessays 24, 175-184.
34. Veitia, R.A. (2003a). Nonlinear effects in macromolecular assembly and dosage sensitivity. J. Theor. Biol. 220, 19-25.
35. Veitia, R.A. (2003b). A sigmoidal transcriptional response: Cooperativity, synergy and dosage effects. Biol. Rev. Camb. Philos. Soc. 78, 149-170.
36. Veitia, R.A. (2004). Gene dosage balance in cellular circuits and pathways: Implications for dominance and gene duplicability. Genetics 168, 569-574.
37. Walsh, J.B. (1995). How often do duplicated genes evolve new functions? Genetics 139, 421-428.
38. Wolfe, K.H. (2001). Yesterday's polyploids and the mystery of diploidization. Nat. Rev. Genet. 2, 333-341.
39. Yang, J., Lusk, R., and Li, W.H. (2003). Organismal complexity, protein complexity, and gene duplicability. Proc. Natl. Acad. Sci. USA 100, 15661-15665.
40. Yu, J., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79-92.