International Journal of
Biodiversity and Conservation

  • Abbreviation: Int. J. Biodivers. Conserv.
  • Language: English
  • ISSN: 2141-243X
  • DOI: 10.5897/IJBC
  • Start Year: 2009
  • Published Articles: 679

Review

Gene duplication: A major force in evolution and bio-diversity

Chandan Roy
  • Chandan Roy
  • Department of Genetics and Plant Breeding, G. B. Pant University of Agriculture and Technology, Pantnagar U S Nagar- 263145, Uttarakhand, India.
  • Google Scholar
Indra Deo
  • Indra Deo
  • Department of Genetics and Plant Breeding, G. B. Pant University of Agriculture and Technology, Pantnagar U S Nagar- 263145, Uttarakhand, India.
  • Google Scholar


  •  Accepted: 26 August 2013
  •  Published: 31 January 2014

References

 

Adams KL, Cronn R, Percifield R, Wendel JF (2003). Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA. 100:4649-4654.
Crossref
 
Adams KL, Wendel JF (2005). Allele-specific, bi-directional silencing of an alcohol dehydrogenase gene in different organs of interspecific diploid cotton hybrids. Genetics 171:2139–2142.
Crossref
 
Adams KL, Percifield R, Wendel JF (2004). Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168: 2217-2226.
Crossref
 
Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815.
Crossref
 
Bailey JA, Liu G, Eichler EE (2003). An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73:823–834.
Crossref
 
Barakat A, Choi A, Yassin NB, Park JS, Sun Z, Carlson JE (2011). Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus. Gene 479 (1-2):37-46.
Crossref
 
Blanc G, Hokamp K, Wolfe KH (2003). A recent polyploidy super-imposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13:137-144.
Crossref
 
Blanc G, Wolfe KH (2004). Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell. 16: 1679–1691.
Crossref
 
Bowers JE, Chapman BA, Rong J, Paterson AH (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-438.
Crossref
 
Bridges CB (1936). The Bar 'gene' a duplication. Science 83:210–211.
Crossref
 
Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T et al. (2006). Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc. Natl Acad. Sci. 103:14959-14964.
Crossref
 
Chapman BA, Bowers JE, Feltus FA, Paterson AH (2006). Buffering crucial functions by paleologous duplicated genes may impart cyclicality to angiosperm genome duplication. Proc. Natl. Acad. Sci. USA 103:2730–35.
Crossref
 
Roth C, Rastogi S, Arvestad L, Dittmar K, Light S, Ekman D,  Liberles DA (2007). Evolution After Gene Duplication: Models, Mechanisms, Sequences, Systems, and Organisms. J. Exp. Zool. B Mol. Dev. Evol. 308(1):58-73.
 
Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L (2005). Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet. 21:673–82.
Pubmed
 
Crane PR, Friis EM, Pedersen KR (1995). The origin and early diver-sification of angiosperms. Nature 374: 27–33.
Crossref
 
Crane PR, Herendeen P, Friis EM (2004). Fossils and plant phylogeny. Am. J. Bot. 91:1683–1699.
Crossref
 
Davies TJ, Barraclough TG, Chase MW, Soltis PS, Soltis DE, Savolainen V (2004). Darwin's abominable mystery: Insights from a super tree of the angiosperms. Proc. Natl. Acad. Sci. USA 101:1904–09.
Crossref
 
Doyle JA, Donoghue MJ (1993). Phylogenies and angiosperm diversification. Paleobiology 19: 141–167.
 
Force A, Cresko WA, Pickett FB, Proulx SR, Amemiya C, Lynch M (1999). The origin of subfunctions and modular gene regulation. Genetics 170:433–46.
Crossref
 
Gaut BS, Doebley JF (1997). DNA sequence evidence for the seg-mental allotetraploid origin of maize. Proc. Natl Acad. Sci. 94: 6809-6814.
Crossref
 
Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92–100.
Crossref
 
Grant V (1981). Plant Speciation. Columbia University Press, New York.
 
Gupta PK (2007). Duplication and Deficiencies. In: Cytogenetics (7th ed.). Rastogi Publication, Meerut. pp.19-43.
 
Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M (2002). Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res. 12: 272–280.
Crossref
 
He P, Friebe B, Gill B, Zhou J-M (2003). Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol Biol. 52:401-414.
Crossref
 
Hughes AL (1994). The evolution of functionally novel proteins after gene duplication. Proc. Biol. Sci. 256:119–124.
Crossref
 
Hurles M (2004). Gene duplication: the genomic trade in spare parts. PloS Biol. 2(7):900–904.
Crossref
 
Hurst LD, Smith NGC (1998). The evolution of concerted evolution. Proc. R. Soc. Lond. Ser. B 265: 121–127.
Crossref
 
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C et al. (2007). The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467.
Crossref
 
Kashkush K, Feldman M, Levy AA (2002). Gene loss, silencing, and activation in a newly synthesized wheat allotetraploid. Genetics 160:1651-1659.
PMid:11973318 PMCid:PMC1462064
 
Kellis M, Birren BW, Lander ES (2004). Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cereviseae. Nature 428:617-624.
Crossref
 
Ku HM, Vision T, Liu J, Tanksley SD (2000). Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl Acad. Sci. 97: 9121-9126.
Crossref
 
Li WH (1997). Molecular Evolution, Sinauer.
 
Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ (2005). Human sub-telomeres are hot spots of inter chromosomal recombination and segmental duplication. Nature 437:94–100.
Crossref
 
Lynch M, Force A (2000). The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459–473.
PMid:10629003 PMCid:PMC1460895
 
Lynch M, Conery JS (2000). The evolutionary fate and consequences of duplicate genes. Science 290: 1151–1155.
Crossref
 
Lynch M, O'Hely M, Walsh B, Force A (2001). The probability of preser-vation of a newly arisen gene duplicate. Genetics 159: 1789–1804
Pubmed
 
Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y (2005). Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. USA 102:5454-5459.
Crossref
 
Masterson J (1994). Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science 264: 421–423.
Crossref
 
Mombaerts P (2001). The human repertoire of odorant receptor genes and pseudogenes. Annu. Rev. Genomics Hum. Genet. 2: 493–510.
Crossref
 
Nei M (2009) Gene duplication and nucleotide substitution in evolution. Nature 221: 40–42.
Crossref
 
Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y, Sun Q, Chen ZJ (2009). Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457: 327–331.
Crossref
 
Nowak MA, Boerlijst MC, Smith JM (1997). Evolution of genetic redundancy. Nature 388:167–171.
Crossref
 
Ohno S (1970). Evolution by Gene Duplication. Springer-Verlag.
Crossref
 
Ota T, Nei M (1995). Evolution of immunoglobulin VH pseudogenes in chickens. Mol. Biol. Evol. 12: 94–102.
Crossref
 
Pan D, Zhang L (2007). Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates. Genome Biol. 8:R158.
Crossref
 
Piontkivska H, Alejandro PR, Masatoshi N (2002). Purifying selection and birth-and-death evolution in the histone H4 gene family. Mol. Biol. Evol. 19: 689–697
Crossref
 
Roulin A, Paul LA, Marc L, Jessica S, Andrew F, Greg M, Gary S, Rebecca WD, Scott AJ (2012). The fate of duplicated genes in a polyploid plant genome. Plant J. 73(1): 143-53.
Crossref
 
Rouquier S, Blancher A, Giorgi D (2000). The olfactory receptor gene repertoire in primates and mouse: evidence for reduction of the functional fraction in primates. Proc. Natl. Acad. Sci. 97: 2870–2874.
Crossref
 
Samonte RV, Eichler EE (2002). Segmental duplications and the evolutionof the primate genome. Nat Rev Genet. 3:65–72.
Crossref
 
Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH (2006). Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341-345.
Crossref
 
Semon M, Wolfe KH (2007). Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor. Trends Genet. 23:108-112.
Crossref
 
Shanks N (2004). God, the Devil, and Darwin, Oxford University Press, NY. p.74.
 
Simillion C, Vandepoele K, Van Montagu MC, Zabeau M, Van de Peer Y (2002). The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 99:13627-13632.
Crossref
 
Sterck L, Rombauts S, Vandepoele K, Rouze P, Peer YV (2007). How many genes are there in plants (. . . and why are they there)? Curr. Opin. Plant Biol. 10:199–203.
Crossref
 
Stuessy TF (2004). A transitional–combinatorial theory for the origin of angiosperms. Taxon. 53:3–16.
Crossref
 
Taylor JS, Peer VD, Meyer A (2001). Genome duplication, divergent resolution and speciation. Trends Genet. 17:299–301.
Crossref
 
Thomas BC, Pedersen B, Freeling M (2006). Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homologue leaving clusters enriched in the sensitive genes. Genome Res. 16:934-946.
Crossref
 
Titov II, Vorozheykin PS (2011). Analysis of miRNA duplication in the human genome and the role of transposon evolution in this process. Russian J. Genet. 1(4): 308-314.
Crossref
 
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596-1604.
Crossref
 
Vinckenbosch N, Dupanloup I, Kaessamann H (2006). Evolutionary fate of retroposed gene copies in the human genome. PNAS 103 (9): 3220-25.
Crossref
 
Walsh JB (1995). How often do duplicated genes evolve new functions? Genetics 139: 421–428.
Pubmed
 
Wang J, Tian L, Madlung A, Lee HS, Chen M, Lee JJ, Watson B, Kagochi T, Comai L, Chen ZJ (2004). Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167:1961-1973.
Crossref
 
Wang Z, Banik M, Cloutier S (2013). Divergent evolutionary mechanisms of co-located Tak/Lrk and Glu-D3 loci revealed by comparative analysis of grass genomes. Genome 56(4):195-204.
Crossref
 
Werth CR, Windham MD (1991). A model for divergent, allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression. Am. Nat. 137:515–526.
Crossref
 
Wing SL, Boucher LD (1998). Ecological aspects of the cretaceous flowering plant radiation. Annu. Rev. Earth Planet Sci. 26: 379–421.
Crossref
 
Wolfe KH, Shields DC (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708–713.
Pubmed
 
Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E (2008). A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319:1527–1530.
Crossref
 
Zhang J (2003). Evolution by gene duplication: an update. Trends Ecol. Evol. 18:192-98.
Crossref
 
Zhang X, Firestein S (2002). The olfactory receptor gene superfamily of the mouse. Nat. Neurosci. 5: 124–133.
Pubmed