[ James A. Shapiro ] James A. Shapiro

Genomic responses to changes in ploidy and interspecific hybridization in fungi, plants and animals

Fungal Taxon

Genomic response

Cryptococcus neoformans

Chromosome loss and recombination  (Li, Averette et al. 2012)

Industrial yeasts

Recombination and mosaic chromosome formation in hybrids  (Querol and Bond 2009)


Chromosome changes and mating incompatibilities in cerevisaea-paradoxus hybrids (Greig, Louis et al. 2002), cerevisiae-uvarum and cerevisiae-kudriavzevii hybrids (Sipiczki 2008) and artificial polyploidy (Maclean and Greig 2011)

Pichia sorbitophila

Genome instability and restructuring (Louis, Despons et al. 2012)

Multiple genera

Genome doubling and restructuring (Albertin and Marullo 2012)



Plant Taxon


Genomic response

Asteraceae (Compositae)




Genome expansion and retrotransposon proliferation in sunflower hybrids (Ungerer, Strakosh et al. 2009)

Chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species (Lai, Nakazato et al. 2005)

Rapid chromosome evolution in polyploids (Lim, Soltis et al. 2008)

Deletions in hybrids and allotetraploids (Buggs, Doust et al. 2009; Tate, Joshi et al. 2009; Buggs, Chamala et al. 2012)


Genome duplication in hybrids (Hegarty, Barker et al. 2006)




Altered methylation patterns and chromosome restructuring in hybrids (Salmon, Ainouche et al. 2005)


Genome instability in hybrids (Marfil, Masuelli et al. 2006)



Nicotiana spp. (tobacco)

Elimination of repeated DNA in a synthetic allotetraploid (Skalicka, Lim et al. 2005)


Intragenic recombination and hybrid speciation (Kelly, Leitch et al. 2010)










Extensive genomic variability induced by introgression from wild rice (Wang, Dong et al. 2005)

LTR retrotransposon movements in rice lines introgressed by wild rice (Shen, Lin et al. 2005)

Retrotransposon activation following introgression (Liu and Wendel 2000)

Incompatible crosspollination leading to transgenerational mobilization of multiple transposable elements (Wang, Chai et al. 2009)

Transpositional activation of mPing in an asymmetric nuclear somatic cell hybrid of rice and Zizania latifolia accompanied by massive element loss. (Shan, Ou et al. 2009)





Rapid genome change in synthetic polyploids (Song, Lu et al. 1995)

Large scale chromosome restructuring (Kantama, Sharbel et al. 2007)



Wheat (Feldman and Levy 2005)








Sequence loss and cytosine methylation following hybridization and allopolyploidy (Shaked, Kashkush et al. 2001)

Rapid genome evolution following allopolyploidy (Ozkan, Levy et al. 2001)

Parental repeat elimination in newly synthesized allopolyploids (Han, Fedak et al. 2005)

Rapid genomic changes in interspecific and intergeneric hybrids and allopolyploids (Han, Fedak et al. 2003)

Amplification of transposable elements (Yaakov and Kashkush 2011)





Chromosome rearrangements after allotetraploid formation (Pontes, Neves et al. 2004)

Aneuploidy and genetic variation in the Arabidopsis thaliana triploid response. (Henry, Dilkes et al. 2005)

Genomic changes in synthetic polyploids (Madlung, Tyagi et al. 2005)

Plants in general

Genome doubling following hybridization (Buggs, Soltis et al. 2009)



Animal Taxon

Genomic Response

Drosophila spp.

Increased retrotransposition in interspecific hybrid (Labrador, Farre et al. 1999)

Macropus marsupials

Centromere instability in interspecific hybrids (Metcalfe, Bulazel et al. 2007)


Chromosome remodeling in interspecific hybrids (O'Neill, O'Neill et al. 1998)


Amplification and double minutes in a hybrid (Brown, Strbuncelj et al. 2002)

Rice fish (medaka)

Chromosome elimination in an interspecific hybrid (Sakai, Konno et al. 2007)

Odontophrynus americanus (amphibian)

Chromosome instabilities and centromere dysfunction in tetraploids (Becak and Becak 1998; Becak and Kobashi 2004)





Albertin, W. and P. Marullo (2012). "Polyploidy in fungi: evolution after whole-genome duplication." Proc Biol Sci 279(1738): 2497-2509. http://www.ncbi.nlm.nih.gov/pubmed/22492065.

Becak, M. L. and W. Becak (1998). "Evolution by polyploidy in Amphibia: new insights." Cytogenet Cell Genet 80(1-4): 28-33. http://www.ncbi.nlm.nih.gov/pubmed/9678330.

Becak, M. L. and L. S. Kobashi (2004). "Evolution by polyploidy and gene regulation in Anura." Genet Mol Res 3(2): 195-212. http://www.ncbi.nlm.nih.gov/pubmed/15266394.

Brown, J. D., M. Strbuncelj, et al. (2002). "Interspecific hybridization induced amplification of Mdm2 on double minutes in a Mus hybrid." Cytogenet Genome Res 98(2-3): 184-188. http://www.ncbi.nlm.nih.gov/pubmed/12698001.

Buggs, R. J., S. Chamala, et al. (2012). "Rapid, Repeated, and Clustered Loss of Duplicate Genes in Allopolyploid Plant Populations of Independent Origin." Curr Biol. http://www.ncbi.nlm.nih.gov/pubmed/22264605.

Buggs, R. J., A. N. Doust, et al. (2009). "Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids." Heredity 103(1): 73-81. http://www.ncbi.nlm.nih.gov/pubmed/19277058.

Buggs, R. J., P. S. Soltis, et al. (2009). "Does hybridization between divergent progenitors drive whole-genome duplication?" Mol Ecol 18(16): 3334-3339. http://www.ncbi.nlm.nih.gov/pubmed/19627486.

Feldman, M. and A. A. Levy (2005). "Allopolyploidy--a shaping force in the evolution of wheat genomes." Cytogenet Genome Res 109(1-3): 250-258. http://www.ncbi.nlm.nih.gov/pubmed/15753584.

Greig, D., E. J. Louis, et al. (2002). "Hybrid speciation in experimental populations of yeast." Science 298(5599): 1773-1775. http://www.ncbi.nlm.nih.gov/pubmed/12459586.

Han, F., G. Fedak, et al. (2005). "Rapid and repeatable elimination of a parental genome-specific DNA repeat (pGc1R-1a) in newly synthesized wheat allopolyploids." Genetics 170(3): 1239-1245. http://www.ncbi.nlm.nih.gov/pubmed/15911583.

Han, F. P., G. Fedak, et al. (2003). "Rapid genomic changes in interspecific and intergeneric hybrids and allopolyploids of Triticeae." Genome 46(4): 716-723. http://www.ncbi.nlm.nih.gov/pubmed/12897878.

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. http://www.ncbi.nlm.nih.gov/pubmed/16920628.

Henry, I. M., B. P. Dilkes, et al. (2005). "Aneuploidy and genetic variation in the Arabidopsis thaliana triploid response." Genetics 170: 1979-1988. http://www.ncbi.nlm.nih.gov/pubmed/15944363.

Kantama, L., T. F. Sharbel, et al. (2007). "Diploid apomicts of the Boechera holboellii complex display large-scale chromosome substitutions and aberrant chromosomes." Proc Natl Acad Sci U S A 104(35): 14026-14031. http://www.ncbi.nlm.nih.gov/pubmed/17704257.

Kelly, L. J., A. R. Leitch, et al. (2010). "Intragenic recombination events and evidence for hybrid speciation in Nicotiana (Solanaceae)." Mol Biol Evol 27(4): 781-799. http://www.ncbi.nlm.nih.gov/pubmed/19897524.

Labrador, M., M. Farre, et al. (1999). "Interspecific hybridization increases transposition rates of Osvaldo." Mol Biol Evol 16(7): 931-937. http://www.ncbi.nlm.nih.gov/pubmed/10406110.

Lai, Z., T. Nakazato, et al. (2005). "Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species." Genetics 171(1): 291-303. http://www.ncbi.nlm.nih.gov/pubmed/16183908.

Li, W., A. F. Averette, et al. (2012). "Genetic Diversity and Genomic Plasticity of Cryptococcus neoformans AD Hybrid Strains." G3 (Bethesda) 2(1): 83-97. http://www.ncbi.nlm.nih.gov/pubmed/22384385.

Lim, K. Y., D. E. Soltis, et al. (2008). "Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae)." PLoS One 3(10): e3353. http://www.ncbi.nlm.nih.gov/pubmed/18843372.

Liu, B. and J. F. Wendel (2000). "Retrotransposon activation followed by rapid repression in introgressed rice plants." Genome 43(5): 874-880. http://www.ncbi.nlm.nih.gov/pubmed/11081978.

Louis, V. L., L. Despons, et al. (2012). "Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization." G3 (Bethesda) 2(2): 299-311. http://www.ncbi.nlm.nih.gov/pubmed/22384408.

Maclean, C. J. and D. Greig (2011). "Reciprocal gene loss following experimental whole-genome duplication causes reproductive isolation in yeast." Evolution 65(4): 932-945. http://www.ncbi.nlm.nih.gov/pubmed/21114494.

Madlung, A., A. P. Tyagi, et al. (2005). "Genomic changes in synthetic Arabidopsis polyploids." Plant J 41(2): 221-230. http://www.ncbi.nlm.nih.gov/pubmed/15634199.

Marfil, C. F., R. W. Masuelli, et al. (2006). "Genomic instability in Solanum tuberosum x Solanum kurtzianum interspecific hybrids." Genome 49(2): 104-113. http://www.ncbi.nlm.nih.gov/pubmed/16498460.

Metcalfe, C. J., K. V. Bulazel, et al. (2007). "Genomic instability within centromeres of interspecific marsupial hybrids." Genetics 177(4): 2507-2517. http://www.ncbi.nlm.nih.gov/pubmed/18073443.

O'Neill, R. J., M. J. O'Neill, et al. (1998). "Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid." Nature 393(6680): 68-72. http://www.ncbi.nlm.nih.gov/pubmed/9590690.

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. http://www.ncbi.nlm.nih.gov/pubmed/11487689.

Pontes, O., N. Neves, et al. (2004). "Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome." Proc Natl Acad Sci U S A 101(52): 18240-18245. http://www.ncbi.nlm.nih.gov/pubmed/15604143.

Querol, A. and U. Bond (2009). "The complex and dynamic genomes of industrial yeasts." FEMS Microbiol Lett 293(1): 1-10. http://www.ncbi.nlm.nih.gov/pubmed/19175410.

Sakai, C., F. Konno, et al. (2007). "Chromosome elimination in the interspecific hybrid medaka between Oryzias latipes and O. hubbsi." Chromosome Res 15(6): 697-709. http://www.ncbi.nlm.nih.gov/pubmed/17603754.

Salmon, A., M. L. Ainouche, et al. (2005). "Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae)." Mol Ecol 14(4): 1163-1175. http://www.ncbi.nlm.nih.gov/pubmed/15773943.

Shaked, H., K. Kashkush, et al. (2001). "Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat." Plant Cell 13(8): 1749-1759. http://www.ncbi.nlm.nih.gov/pubmed/11487690.

Shan, X. H., X. F. Ou, et al. (2009). "Transpositional activation of mPing in an asymmetric nuclear somatic cell hybrid of rice and Zizania latifolia was accompanied by massive element loss." Theor Appl Genet 119(7): 1325-1333. http://www.ncbi.nlm.nih.gov/pubmed/19711051.

Shen, Y., X. Lin, et al. (2005). "Genomic rearrangement in endogenous long terminal repeat retrotransposons of rice lines introgressed by wild rice (Zizania latifolia Griseb.)." Journal  of Integrative Plant Biology 47(8): 998-1008. .

Sipiczki, M. (2008). "Interspecies hybridization and recombination in Saccharomyces wine yeasts." FEMS Yeast Res 8(7): 996-1007. http://www.ncbi.nlm.nih.gov/pubmed/18355270.

Skalicka, K., K. Y. Lim, et al. (2005). "Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco." New Phytol 166(1): 291-303. http://www.ncbi.nlm.nih.gov/pubmed/15760371.

Song, K., P. Lu, et al. (1995). "Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution." Proc Natl Acad Sci U S A 92(17): 7719-7723. http://www.ncbi.nlm.nih.gov/pubmed/7644483.

Tate, J. A., P. Joshi, et al. (2009). "On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae)." BMC Plant Biol 9: 80. http://www.ncbi.nlm.nih.gov/pubmed/19558696.

Ungerer, M. C., S. C. Strakosh, et al. (2009). "Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data." BMC Biol 7: 40. http://www.ncbi.nlm.nih.gov/pubmed/19594956.

Wang, H., Y. Chai, et al. (2009). "Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability." BMC Plant Biol 9: 63. http://www.ncbi.nlm.nih.gov/pubmed/19476655.

Wang, Y. M., Z. Y. Dong, et al. (2005). "Extensive de Novo genomic variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.)." Genetics 170(4): 1945-1956. http://www.ncbi.nlm.nih.gov/pubmed/15937131.

Yaakov, B. and K. Kashkush (2011). "Methylation, transcription, and rearrangements of transposable elements in synthetic allopolyploids." Int J Plant Genomics 2011: 569826. http://www.ncbi.nlm.nih.gov/pubmed/21760771.