Table 5D. Whole genome duplications or other amplifications observed in the genome sequence record

Organism or Taxon


Yeast (Saccharomyces cerevisiae)

(Fusco, Grassi et al. 2010)

Fungi (Rhizopus oryzae, rice pathogen, and Mycosphaerella graminicola, wheat pathogen)

(Ma, Ibrahim et al. 2009; Albertin and Marullo 2012)

(Stukenbrock, Jorgensen et al. 2010)

Paramecium tetraurelia (3 rounds of WGD)

(Aury 2006)


(De Bodt, Maere et al. 2005; Cui, Wall et al. 2006; Soltis 2009; Coate and Doyle 2011)


(Seoighe and Gehring 2004; Casneuf, De Bodt et al. 2006; Paterson, Chapman et al. 2006; Zhang, Huang et al. 2010)

Rice and other cereals (Poaceae)

(Tian, Xiong et al. 2005; Paterson, Chapman et al. 2006)

Wheat (Triticum)

(Ozkan, Levy et al. 2001; Feldman and Levy 2009)

Maize (Zea mays)

(Woodhouse, Schnable et al. 2010; Schnable, Springer et al. 2011)

Ragwort (Senecio)

(Hegarty, Barker et al. 2006; Hegarty, Batstone et al. 2011)

Fireweed (Chamerion angustifolium)

(Maherali, Walden et al. 2009)

Apple (Malus)

(Considine, Wan et al. 2012)

Salsify (Tragopogon, Asteraceae)

(Buggs, Chamala et al. 2010)


(Hufton, Groth et al. 2008; Hughes and Liberles 2008; Kassahn, Dang et al. 2009)

Teleost fishes (Fugu, Tetraodon nigroviridis)

(Christoffels, Koh et al. 2004; Jaillon 2004; Brunet 2006; Kuraku and Meyer 2009)


(Mungpakdee, Seo et al. 2008)




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Aury, J. M. (2006). "Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia." Nature 444: 171-178. .

Brunet, F. G. (2006). "Gene loss and evolutionary rates following whole-genome duplication in teleost fishes." Mol. Biol. Evol. 23: 1808-1816.

Buggs, R. J., S. Chamala, et al. (2010). "Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping." Mol Ecol 19 Suppl 1: 132-146.

Casneuf, T., S. De Bodt, et al. (2006). "Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana." Genome Biol 7(2): R13.

Christoffels, A., E. G. Koh, et al. (2004). "Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes." Mol. Biol. Evol. 21: 1146-1151. .

Coate, J. E. and J. J. Doyle (2011). "Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications." Plant Signal Behav 6(4): 594-597.

Considine, M. J., Y. Wan, et al. (2012). "Molecular genetic features of polyploidization and aneuploidization reveal unique patterns for genome duplication in diploid Malus." PLoS One 7(1): e29449.

Cui, L., P. K. Wall, et al. (2006). "Widespread genome duplications throughout the history of flowering plants." Genome Res 16(6): 738-749.

De Bodt, S., S. Maere, et al. (2005). "Genome duplication and the origin of angiosperms." Trends Ecol. Evol. 20: 591-597. .

Feldman, M. and A. A. Levy (2009). "Genome evolution in allopolyploid wheat--a revolutionary reprogramming followed by gradual changes." J Genet Genomics 36(9): 511-518.

Fusco, D., L. Grassi, et al. (2010). "Ordered structure of the transcription network inherited from the yeast whole-genome duplication." BMC Syst Biol 4: 77.

Hegarty, M. J., G. L. Barker, et al. (2006). "Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication." Curr Biol 16(16): 1652-1659.

Hegarty, M. J., T. Batstone, et al. (2011). "Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae)." Mol Ecol 20(1): 105-113.

Hufton, A. L., D. Groth, et al. (2008). "Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement." Genome Res 18(10): 1582-1591.

Hughes, T. and D. A. Liberles (2008). "Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species." J Mol Evol 67(4): 343-357.

Jaillon, O. (2004). "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype." Nature 431: 946-957. .

Kassahn, K. S., V. T. Dang, et al. (2009). "Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates." Genome Res 19(8): 1404-1418.

Kuraku, S. and A. Meyer (2009). "The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication." Int J Dev Biol 53(5-6): 765-773.

Ma, L. J., A. S. Ibrahim, et al. (2009). "Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication." PLoS Genet 5(7): e1000549.

Maherali, H., A. E. Walden, et al. (2009). "Genome duplication and the evolution of physiological responses to water stress." New Phytol 184(3): 721-731.

Mungpakdee, S., H. C. Seo, et al. (2008). "Differential evolution of the 13 Atlantic salmon Hox clusters." Mol Biol Evol 25(7): 1333-1343.

Ozkan, H., A. A. Levy, et al. (2001). "Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group." Plant Cell 13(8): 1735-1747.

Paterson, A. H., B. A. Chapman, et al. (2006). "Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon." Trends Genet 22(11): 597-602.

Schnable, J. C., N. M. Springer, et al. (2011). "Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss." Proc Natl Acad Sci U S A 108(10): 4069-4074.

Seoighe, C. and C. Gehring (2004). "Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome." Trends Genet. 20: 461-464. .

Soltis, D. E. (2009). "Polyploidy and angiosperm diversification." Am. J. Bot. 96: 336-348. .

Stukenbrock, E. H., F. G. Jorgensen, et al. (2010). "Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola." PLoS Genet 6(12): e1001189.

Tian, C. G., Y. Q. Xiong, et al. (2005). "Evidence for an ancient whole-genome duplication event in rice and other cereals." Yi Chuan Xue Bao 32(5): 519-527.

Woodhouse, M. R., J. C. Schnable, et al. (2010). "Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs." PLoS Biol 8(6): e1000409.

Zhang, P. G., S. Z. Huang, et al. (2010). "Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis." Mol Biol Evol 27(7): 1686-1697.