Natural pathways to polyploidy in plants and consequences for genome reorganization

Cytogenetic and Genome Research

Volumn 140, Issue 2-4, 2013, Pages 79-96

  Tayale A ^a   Parisod, C ^a  

^a UNIVERSITY OF NEUCHÂTEL   (Switzerland)

Author keywords

Chromosome pairing; Dobzhansky Muller incompatibility; Genome evolution; Genome merging; Genome restructuring; Hybrid dysregulation; Speciation; Transposable elements; Unreduced gametes; Whole genome doubling

Indexed keywords

ALLOPOLYPLOIDY; ARTICLE; GENETIC ORGANIZATION; GENETIC VARIABILITY; GENOME; HYBRID DYSGENESIS; NONHUMAN; PLANT; POLYPLOIDY; PRIORITY JOURNAL; SPECIES DIFFERENTIATION; TRANSPOSON;

ANIMALIA;

EID: 84881127570     PISSN: 14248581     EISSN: 1424859X     Source Type: Journal    
DOI: 10.1159/000351318     Document Type: Article

References (191)

1. Abbott R, Lowe A: Origins, establishment and evolution of new polyploid species: Senecio cambrensis and S. eboracensis in the British Isles. Biol J Linn Soc Lond 82: 467-474 (2004).
2. Abbott R, Albach D, Ansell S, Arntzen JW, Baird SJ, et al: Hybridization and speciation. J Evol Biol 26: 229-246 (2013).
3. Adams K, Cronn R, Percifield R, Wendel J: Genes duplicated by polyploidy show unequal contributions to the transcriptome and organspecific reciprocal silencing. Proc Natl Acad Sci USA 100: 4649-4654 (2003).
4. Albertin W, Brabant P, Catrice O, Eber F, Jenczewski E, et al: Autopolyploidy in cabbage ( Brassica oleracea L.) does not alter significantly the proteomes of green tissues. Proteomics 5: 2131-2139 (2005).
5. Albertin W, Alix K, Balliau T, Brabant P, Davanture M, et al: Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization. BMC Genomics 8: 56 (2007).
6. Arrigo N, Barker MS: Rarely successful polyploids and their legacy in plant genomes. Curr Op Pl Biol 15: 140-146 (2012).
7. Arrigo N, Felber F, Parisod C, Buerki S, Alvarez N, et al: Origin and expansion of the allotetraploid Aegilops geniculata , a wild relative of wheat. New Phytol 187: 1170-1180 (2010).
8. Aversano R, Di Dato F, Di Matteo A, Frusciante L, Carputo D: AFLP analysis to assess genomic stability in Solanum regenerants derived from wild and cultivated species. Plant Biotech Rep 5: 265-271 (2011).
9. Beaulieu J, Jean M, Belzile F: The allotetraploid Arabidopsis thaliana-Arabidopsis lyrata subsp. petraea as an alternative model system for the study of polyploidy in plants. Mol Genet Gen 281: 421-435 (2009).
10. Bever JD, Felber F: The theoretical population genetics of polyploidy. Oxford Surv Evol Biol 8: 185-217 (1992).
11. Bikard D, Patel D, Le Metté C, Giorgi V, Camilleri C, et al: Divergent evolution of duplicate genes leads to genetic incompatibilities within A. Thaliana . Science 323: 623-626 (2009).
12. Birchler JA, Veitia RA: Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci USA 109: 14746-14753 (2012).
13. Blanc G, Wolfe K: Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678 (2004).
14. Bourc'his D, Voinnet O: A small-RNA perspective on gametogenesis, fertilization, and early zygotic development. Science 330: 617-622 (2010).
15. Bretagnolle F: Pollen production and spontaneous polyploidization in diploid populations of Anthoxanthum alpinum. Biol J Linn Soc 72: 241-247 (2001).
16. Bretagnolle F, Thompson J: Gametes with the stomatic chromosome number: mechanisms of their formation and role in the evolution of autopolypoid plants. New Phytol 129: 1-22 (1995).
17. Brink RA, Cooper DC: The endosperm in seed development. Bot Rev 13: 479-541 (1947).
18. Brochmann C, Soltis PS, Soltis DE: Multiple origins of the octoploid Scandinavian endemic Draba cacuminum : electrophoretic and morphological evidence. Nord J Bot 12: 257-272 (1992).
19. Brownfield L, Köhler C: Unreduced gamete formation in plants: mechanisms and prospects. J Exp Bot 62: 1659-1668 (2011).
20. Buggs RJA, Doust A, Tate J, Koh J, Soltis K, et al: Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity 103: 73-81 (2009).
21. Buggs RJA, Soltis PS, Soltis DE: Biosystematic relationships and the formation of polyploids. Taxon 60: 324-332 (2011).
22. Buggs RJA, Chamala S, Wu W, Tate JA, Schnable PS, et al: Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Curr Biol 22: 248-252 (2012).
23. Butruille DV, Boiteux LS: Selection-mutation balance in polysomic tetraploids: impact of double reduction and gametophytic selection on the frequency and subchromosomal localization of deleterious mutations. Proc Natl Acad Sci USA 97: 6608-6613 (2000).
24. Chantret N, Salse J, Sabot F, Rahman S, Bellec A, et al: Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops) . Plant Cell 17: 1033-1045 (2005).
25. Chapman MA, Abbott RJ: Introgression of fitness genes across a ploidy barrier. New Phytol 186: 63-71 (2010).
26. Chelaifa H, Monnier A, Ainouche M: Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae). New Phytol 186: 161-174 (2010).
27. Chester M, Gallagher JP, Symonds VV, Cruz da Silva AV, Mavrodiev EV, et al: Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc Natl Acad Sci USA 109: 1176-1181 (2012).
28. Church SA, Spaulding EJ: Gene expression in a wild autopolyploid sunflower series. J Hered 100: 491-495 (2009).
29. Cifuentes M, Grandont L, Moore G, Chevre AM, Jenczewski E: Genetic regulation of meiosis in polyploid species: new insights into an old question. New Phytol 186: 29-36 (2010).
30. Clausen J, Keck DD, Hiesey WM: Plant Evolution through Amphiploidy and Autoploidy, with Examples from the Madiinae (Carnegie Institution of Washington, Washington 1945).
31. Comai L: The advantages and disadvantages of being polyploid. Nat Rev Genet 6: 836-846 (2005).
32. Coyne J, Orr H: Speciation (Sinauer Associates, Sunderland 2004).
33. d'Erfurth I, Jolivet S, Froger N, Catrice O, Novatchkova M, et al: Mutations in AtPS1 ( Arabidopsis thaliana Parallel Spindle 1) lead to the production of diploid pollen grains. PLoS Genet 4:e1000274 (2008).
34. Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, et al: Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet 42: 443-461 (2008).
35. Ehrendorfer F: Polyploidy and distribution, in Lewis WH (ed): Polyploidy. Biological Relevance, pp 45-60 (Plenum Press, New York 1980).
36. Eilam T, Anikster Y, Millet E, Manisterski J, Feldman M: Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum . Genome 51: 616-627 (2008).
37. Eilam T, Anikster Y, Millet E, Manisterski J, Feldman M: Genome size in natural and synthetic autopolyploids and in a natural segmental allopolyploid of several Triticeae species. Genome 52: 275-285 (2009).
38. Eilam T, Anikster Y, Millet E, Manisterski J, Feldman M: Genome size in diploids, allopolyploids, and autopolyploids of mediterranean Triticeae. J Bot 2010:ID341380 (2010).
39. Favarger C: Cytogeography and biosystematics, in Grant WF (ed): Plant Biosystematics, pp 453-476 (Academic Press, Vancouver 1984).
40. Fedoroff NV: Transposable elements, epigenetics, and genome evolution. Science 338: 758-767 (2012).
41. Felber F: Establishment of a tetraploid cytotype in a diploid poplation: effect of relative fitness of the cytotypes. J Evol Biol 4: 195-207 (1991).
42. Feldman M, Levy A, Chalhoub B, Kashkush K: Genomic plasticity in polyploid wheat, in Soltis PS, Soltis DE (eds): Polyploidy and Genome Evolution, pp 109-135 (Springer, Berlin Heidelberg 2012).
43. Flagel L, Udall J, Nettleton D, Wendel J: Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biol 6: 16 (2008).
44. Force A, Lynch M, Pickett F, Amores A, Yan Y, Postlethwait J: Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545 (1999).
45. Fulneček J, Matyášek R, Kovařík A: Faithful inheritance of cytosine methylation patterns in repeated sequences of the allotetraploid tobacco correlates with the expression of DNA methyltransferase gene families from both parental genomes. Mol Genet Genomics 281: 407-420 (2009).
46. Gaeta RT, Pires JC: Homeologous recombination in allopolyploids: the polyploid ratchet. New Phytol 186: 18-28 (2010).
47. Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC: Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19: 3403-3417 (2007).
48. Grant V: Plant Speciation (Columbia University Press, New York 1981).
49. Griffiths S, Sharp R, Foote TN, Bertin I, Wanous M, et al: Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439: 749-752 (2006).
50. Grover CE, Yu Y, Wing RA, Paterson AH, Wendel JF: A phylogenetic analysis of indel dynamics in the cotton genus. Mol Biol Evol 25: 1415-1428 (2008).
51. Grover CE, Gallagher JP, Szadkowski EP, Yoo MJ, Flagel LE, Wendel JF: Homoeolog expression bias and expression level dominance in allopolyploids. New Phytol 196: 966-971 (2012).
52. Han FP, Fedak G, Ouellet T, Liu B: Rapid genomic changes in interspecific and intergeneric hybrids and allopolyploids of Triticeae. Genome 46: 716-723 (2003).
53. Han FP, Fedak G, Guo WL, Liu B: Rapid and repeatable elimination of a parental genomespecific DNA repeat (pGcIR-1a) in newly synthesized wheat allopolyploids. Genetics 170: 1239-1245 (2005).
54. Harlan J, DeWet J: On O. Winge and a prayer: the origins of polyploidy. Bot Rev 41: 361-390 (1975).
55. Hauber DP, Reeves A, Stack SM: Synapsis in a natural autotetraploid. Genome 42: 936-949 (1999).
56. He L, Dooner HK: Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions. Proc Natl Acad Sci USA 106: 8410-8416 (2009).
57. Hegarty M, Hiscock S: Genomic clues to the evolutionary success of polyploid plants. Curr Biol 18:R435-R444 (2008).
58. Hegarty M, Barker G, Wilson I, Abbott R, Edwards K, Hiscock S: Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Curr Biol 16: 1652-1659 (2006).
59. Higgins J, Magusin A, Trick M, Fraser F, Bancroft I: Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus . BMC Genomics 13: 247 (2012).
60. Hu G, Hawkins JS, Grover CE, Wendel JF: The history and disposition of transposable elements in polyploid Gossypium . Genome 53: 599-607 (2010).
61. Husband B: The role of triploid hybrids in the evolutionary dynamics of mixed-ploidy populations. Biol J Linn Soc 82: 537-546 (2004).
62. Innan H, Kondrashov F: The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11: 97-108 (2010).
63. Jackson RC: Polyploidy and diploidy: new perspectives on chromosome paring and its evolutionary implications. Am J Bot 69: 1512-1523 (1982).
64. Jackson RC, Jackson JW: Gene segregation in autotetraploids: prediction from meiotic configurations. Am J Bot 83: 673-678 (1996).
65. Jakobsson M, Hagenblad J, Tavaré S, Säll T, Halldén C, et al: A unique recent origin of the allotetraploid species Arabidopsis suecica : evidence from nuclear DNA markers. Mol Biol Evol 23: 1217-1231 (2006).
66. Jenczewski E, Alix K: From diploids to allopolyploids: the emergence of efficient pairing control genes in plants. Crit Rev Pl Sci 23: 21-45 (2004).
67. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, et al: Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100 (2011).
68. Johnston JS, Pepper AE, Hall AE, Chen ZJ, Hodnett G, et al: Evolution of genome size in Brassicaceae. Ann Bot 95: 229-235 (2005).
69. Johnston SA, Dennijs TPM, Peloquin SJ, Hanneman RE: The significance of genic balance to endosperm development in interspecific crosses. Theor Appl Genet 57: 5-9 (1980).
70. Kashkush K, Feldman M, Levy AA: Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160: 1651-1659 (2002).
71. Kashkush K, Feldman M, Levy AA: Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33: 102-106 (2003).
72. Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, et al: Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics 188: 263-272 (2011).
73. Koh J, Soltis PS, Soltis DE: Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae). BMC Genomics 11: 97 (2010).
74. Koh J, Chen S, Zhu N, Yu F, Soltis PS, Soltis DE: Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents. New Phytol 196: 292-305 (2012).
75. Köhler C, Mittelsten Scheid O, Erilova A: The impact of the triploid block on the origin and evolution of polyploid plants. Trends Genet 26: 142-148 (2010).
76. Koukalova B, Moraes AP, Renny-Byfield S, Matyasek R, Leitch AR, Kovarik A: Fall and rise of satellite repeats in allopolyploids of Nicotiana over c. 5 million years. New Phytol 186: 148-160 (2010).
77. Kovarik A, Renny-Byfield S, Grandbastien MA, Leitch AR: Evolutionary implications of genome and karyotype restructuring in Nicotiana tabacum L, in Soltis PS, Soltis DE (eds): Polyploidy and Genome Evolution, pp 209-224 (Springer, Berlin Heidelberg 2012).
78. Kraitshtein Z, Yaakov B, Khasdan V, Kashkush K: Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat. Genetics 186: 801-812 (2010).
79. Landergott U, Naciri Y, Schneller JJ, Holderegger R: Allelic configuration and polysomic inheritance of highly variable microsatellites in tetraploid gynodioecious Thymus praecox agg. Theor Appl Genet 113: 453-465 (2006).
80. Le Comber SC, Ainouche ML, Kovarik A, Leitch AR: Making a functional diploid: from polysomic to disomic inheritance. New Phytol 186: 113-122 (2010).
81. Leitch AR, Leitch IJ: Genomic plasticity and the diversity of polyploid plants. Science 320: 481-483 (2008).
82. Leitch IJ, Bennett MD: Genome downsizing in polyploid plants. Biol J Linn Soc 82: 651-663 (2004).
83. Leitch IJ, Hanson L, Lim KY, Kovarik A, Chase MW, et al: The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Ann Bot 101: 805-814 (2008).
84. Levin D: Minority cytotype exclusion in local plant populations. Taxon 24: 35-43 (1975).
85. Levin D: The Role of Chromosomal Change in Plant Evolution (Oxford University Press, New York 2002).
86. Levin D: The long wait for hybrid sterility in flowering plants. New Phytol 196: 666-670 (2012).
87. Lewis W: Polyploidy in species populations, in Lewis WH (ed): Polyploidy. Biological Relevance, pp 103-144 (Plenum Press, New York 1980).
88. Li X, Yu E, Fan C, Zhang C, Fu T, Zhou Y: Developmental, cytological and transcriptional analysis of autotetraploid Arabidopsis . Planta 236: 579-596 (2012).
89. Lim KY, Matyasek R, Kovarik A, Leitch AR: Genome evolution in allotetraploid Nicotiana . Biol J Linn Soc 82: 599-606 (2004).
90. Lim KY, Kovarik A, Matyasek R, Chase M, Clarkson J, et al: Sequence of events leading to nearcomplete genome turnover in allopolyploid Nicotiana within five million years. New Phytol 175: 756 (2007).
91. Lim KY, Soltis DE, Soltis PS, Tate J, Matyasek R, et al: Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). PLoS One 3:e3353 (2008).
92. Lin BY: Ploidy barrier to endosperm development in maize. Genetics 107: 103-115 (1984).
93. Liu B, Vega JM, Segal G, Abbo S, Rodova M, Feldman M: Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops . I. Changes in low-copy noncoding DNA sequences. Genome 41: 272-277 (1998).
94. Lu B, Pan X, Zhang L, Huang B, Sun L, et al: A genome-wide comparison of genes responsive to autopolyploidy in Isatis indigotica using Arabidopsis thaliana Affymetrix genechips. Plant Mol Biol Rep 24: 197-204 (2006).
95. Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, Osborn T: Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol 140: 336-348 (2006).
96. Luo ZW, Zhang Z, Leach L, Zhang RM, Bradshaw JE, Kearsey MJ: Constructing genetic linkage maps under a tetrasomic model. Genetics 172: 2635-2645 (2006).
97. Lynch M: The Origins of Genome Architecture (Sinauer Associates Inc., Sunderland 2007).
98. Ma XF, Gustafson J: Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenet Genome Res 109: 236-249 (2005).
99. Mable BK: Breaking down taxonomic barriers in polyploidy research. Trends Plant Sci 8: 582-590 (2003).
100. Mable BK: 'Why polyploidy is rarer in animals than in plants': myths and mechanisms. Biol J Linn Soc 82: 453-466 (2004).
101. Mable BK, Alexandrou MA, Taylor MI: Genome duplication in amphibians and fish: an extended synthesis. J Zool 284: 151-182 (2011).
102. Madlung A, Tyagi AP, Watson B, Jiang H, Kagochi T, et al: Genomic changes in synthetic Arabidopsis polyploids. Plant J 41: 221-230 (2005).
103. Maheshwari S, Barbash DA: The genetics of hybrid incompatibilities. Annu Rev Genet 45: 331-355 (2011).
104. Mandáková T, Lysak MA: Chromosomal phylogeny and karyotype evolution in x = 7 crucifer species (Brassicaceae). Plant Cell 20: 2559-2570 (2008).
105. Martelotto LG, Ortiz JPA, Stein J, Espinoza F, Quarin CL, Pessino SC: A comprehensive analysis of gene expression alterations in a newly synthesized Paspalum notatum autotetraploid. Plant Sci 169: 211-220 (2005).
106. Martelotto LG, Ortiz JPA, Stein J, Espinoza F, Quarin CL, Pessino SC: Genome rearrangements derived from autopolyploidization in Paspalum sp. Plant Sci 172: 970-977 (2007).
107. Martienssen RA: Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis . New Phytol 186: 46-53 (2010).
108. Mason A, Nelson M, Yan G, Cowling W: Production of viable male unreduced gametes in Brassica interspecific hybrids is genotype specific and stimulated by cold temperatures. BMC Plant Biol 11: 103 (2011).
109. Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, et al: Recently formed polyploid plants diversify at lower rates. Science 333: 1257 (2011).
110. McGrath CL, Lynch M: Evolutionary significance of whole-genome duplication, in Soltis PS, Soltis DE (eds): Polyploidy and Genome Evolution, pp 1-20 (Springer, Berlin Heidelberg 2012).
111. Mestiri I, Chagué V, Tanguy AM, Huneau C, Huteau V, et al: Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity. New Phytol 186: 86-101 (2010).
112. Mizuta Y, Harushima Y, Kurata N: Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes. Proc Natl Acad Sci USA 107: 20417-20422 (2010).
113. Modliszewski JL, Willis JH: Allotetraploid Mimulus sookensis are highly interfertile despite independent origins. Mol Ecol 21: 5280-5298 (2012).
114. Muntzing A: Multiplication of chromosomes in galeopis crossbreeds and their phylogenetic significance. Hereditas 14: 153-172 (1930).
115. Muntzing A: The evolutionary significance of autopolyploidy. Hereditas 21: 363-378 (1936).
116. Nei M, Nozawa M: Roles of mutation and selection in speciation: from Hugo de Vries to the modern genomic era. Genome Biol Evol 3: 812-829 (2011).
117. Ng DWK, Zhang C, Miller M, Shen Z, Briggs SP, Chen ZJ: Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity (Edinb) 108: 419-430 (2012).
118. Noor MAF, Feder JL: Speciation genetics: evolving approaches. Nat Rev Genet 7: 851-861 (2006).
119. Ohno S: Evolution by Gene Duplication (Springer Verlag, Berlin 1970).
120. Oka HI: Genetic analysis for the sterility of hybrids between distantly related varieties of cultivated rice. J Genet 55: 397-409 (1957).
121. Otto S: The evolutionary consequences of polyploidy. Cell 131: 452-462 (2007).
122. Otto S, Whitton J: Polyploid incidence and evolution. Annu Rev Genet 34: 401-437 (2000).
123. Ozkan H, Levy AA, Feldman M: Allopolyploidyinduced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13: 1735-1747 (2001).
124. Ozkan H, Tuna M, Arumuganathan K: Nonadditive changes in genome size during allopolyploidization in the wheat (Aegilops-Triticum) group. J Hered 94: 260-264 (2003).
125. Ozkan H, Tuna M, Galbraith DW: No DNA loss in autotetraploids of Arabidopsis thaliana . Plant Breed 125: 288-291 (2006).
126. Parisod C: Polyploids integrate genomic changes and ecological shifts. New Phytol 193: 297-300 (2012).
127. Parisod C, Besnard G: Glacial in situ survival in the Western Alps and polytopic autopolyploidy in Biscutella laevigata L. (Brassicaceae). Mol Ecol 16: 2755-2767 (2007).
128. Parisod C, Senerchia N: The response of transposable elements to polyploidy, in Grandbastien MA, Casacuberta JM (eds): Plant Transposable Elements, Topics in Current Genetics, pp 147-168 (Springer, Berlin Heidelberg 2013).
129. Parisod C, Holderegger R, Brochmann C: Evolutionary consequences of autopolyploidy. New Phytol 186: 5-17 (2010).
130. Parisod C, Alix K, Just J, Petit M, Sarilar V, et al: Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol 186: 37-45 (2010).
131. Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien MA, Ainouche M: Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina . New Phytol 184: 1003-1015 (2009).
132. Parisod C, Mhiri C, Lim KY, Clarkson JJ, Chase MW, et al: Differential dynamics of transposable elements during long-term diploidization of Nicotiana Section Repandae (Solanaceae) allopolyploid genomes. PLoS One 7: e50352 (2012).
133. Petit C, Bretagnolle F, Felber F: Evolutionary consequences of diploid-polyploid hybrid zones in wild species. Trends Ecol Evol 14: 306-311 (1999).
134. Petit M, Lim KY, Julio E, Poncet C, Dorlhac de Borne F, et al: Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum) . Mol Genet Genomics 278: 1-15 (2007).
135. Petit M, Guidat C, Daniel J, Denis E, Montoriol E, et al: Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol 186: 135-147 (2010).
136. Pires JC, Zhao J, Schranz ME, Leon EJ, Quijada PA, et al: Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol J Linn Soc 82: 675-688 (2004).
137. Qi B, Huang W, Zhu B, Zhong X, Guo J, et al: Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines. BMC Biol 10: 3 (2012).
138. Raina SN, Parida A, Koul KK, Salimath SS, Bisht MS, et al: Associated chromosomal DNA changes in polyploids. Genome 37: 560-564 (1994).
139. Ramsey J: Unreduced gametes and neopolyploids in natural populations of Achillea borealis . Heredity 98: 143-150 (2007).
140. Ramsey J, Schemske DW: Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu Rev Ecol Syst 29: 467-501 (1998).
141. Ramsey J, Schemske DW: Neopolyploidy in flowering plants. Annu Rev Ecol Syst 33: 589-639 (2002).
142. Renny-Byfield S, Chester M, Kovařík A, Le Comber SC, Grandbastien MA, et al: Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum , predominantly through the elimination of paternally derived repetitive DNAs. Mol Biol Evol 28: 2843-2854 (2011).
143. Riddle N, Jiang H, An L, Doerge R, Birchler J: Gene expression analysis at the intersection of ploidy and hybridity in maize. Theor Appl Genet 120: 341-353 (2010).
144. Rieseberg LH: Polyploid evolution: keeping the peace at genomic reunions. Curr Biol 11:R925-R928 (2001).
145. Rieseberg LH: Chromosomal rearrangements and speciation. Trends Ecol Evol 16: 351-358 (2001).
146. Rieseberg LH, Willis JH: Plant speciation. Science 317: 910-914 (2007).
147. Rivero-Guerra AO: Cytogenetics, geographical distribution, and pollen fertility of diploid and tetraploid cytotypes of Santolina pectinata Lag. (Asteraceae: Anthemideae). Bot J Linn Soc 156: 657-667 (2008).
148. Ronfort J, Jenczewski E, Bataillon T, Rousset F: Analysis of population structure in autotetraploid species. Genetics 150: 921-930 (1998).
149. Salina EA, Numerova OM, Ozkan H, Feldman M: Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat. Genome 47: 860-867 (2004).
150. Santos JL, Alfaro D, Sanchez-Moran E, Armstrong SJ, Franklin FCH, Jones GH: Partial diploidization of meiosis in autotetraploid Arabidopsis thaliana . Genetics 165: 1533-1540 (2003).
151. Segraves KA, Thompson JN, Soltis PS, Soltis DE: Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia. Mol Ecol 8: 253-262 (1999).
152. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy A: Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749-1759 (2001).
153. Shore JS: Tetrasomic inheritance and isozyme variation in Turnera ulmifolia vars. elegans Urb. and intermedia Urb. (Turneraceae). Heredity 66: 305-312 (1991).
154. Skalická K, Lim KY, Matyasek R, Matzke M, Leitch AR, Kovarik A: Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco. New Phytol 166: 291-303 (2005).
155. Slotkin RK, Martienssen R: Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285 (2007).
156. Slotte T, Huang H, Lascoux M, Ceplitis A: Polyploid speciation did not confer instant reproductive isolation in Capsella (Brassicaceae). Mol Biol Evol 25: 1472-1481 (2008).
157. Soltis DE, Soltis PS: Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol 14: 348-352 (1999).
158. Soltis DE, Soltis PS: Polyploidy and Genome Evolution (Springer, Berlin Heidelberg 2012).
159. Soltis DE, Soltis PS, Pires J, Kovarik A, Tate J, Mavrodiev E: Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogentic, genomic and genetic comparisons. Biol J Linn Soc Lond 82: 485-501 (2004).
160. Soltis DE, Soltis PS, Schemske DW, Hancock JF, Thompson JN, et al: Autopolyploidy in angiosperms: have we grossly underestimated the number of species? Taxon 56: 13-30 (2007).
161. Soltis DE, Buggs RA, Doyle JJ, Soltis PS: What we still don't know about polyploidy. Taxon 59: 1387-1403 (2010).
162. Soltis DE, Buggs RA, Barbazuk WB, Chamala S, Chester M, et al: The early stages of polyploidy: rapid and repeated evolution in Tragopogon , in Soltis PS, Soltis DE (eds): Polyploidy and Genome Evolution, pp 271-292 (Springer, Berlin Heidelberg 2012).
163. Song KM, Lu P, Tang KL, Osborn TC: Rapid genome change in synthetic polyploids of Brassica and its implication for polyploid evolution. Proc Natl Acad Sci USA 92: 7719-7723 (1995).
164. Stebbins G: The inviability, weakness, and sterility of interspecific hybrids. Adv Genet 9: 147 (1958).
165. Stebbins GL: Types of polyploids: their classification and significance. Adv Genet 1: 403-429 (1947).
166. Stebbins GL: Chromosomal Evolution in Higher Plants (Edward Arnold, London 1971).
167. Stewart MN, Dawson DS: Changing partners: moving from non-homologous to homologous centromere pairing in meiosis. Trends Genet 24: 564-573 (2008).
168. Stift M, Berenos C, Kuperus P, van Tienderen PH: Segregation models for disomic, tetrasomic and intermediate inheritance in tetraploids: a general procedure applied to Rorippa (Yellow Cress) microsatellite data. Genetics 179: 2113-2123 (2008).
169. Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, et al: Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 176: 2055-2067 (2007).
170. Szadkowski E, Eber F, Huteau V, Lodé M, Coriton O, et al: Polyploid formation pathways have an impact on genetic rearrangements in resynthesized Brassica napus . New Phytol 191: 884-894 (2011).
171. Tate JA, Ni Z, Scheen AC, Koh J, Gilbert CA, et al: Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 173: 1599-1611 (2006).
172. Tenaillon MI, Hollister JD, Gaut BS: A triptych of the evolution of plant transposable elements. Trends Plant Sci 15: 471-478 (2010).
173. Wang J, Tian L, Madlung A, Lee HS, Chen M, et al: Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167: 1961-1973 (2004).
174. Wang J, Tian L, Lee HS, Wei N, Jiang H, et al: Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172: 507-517 (2006).
175. Weiss H, Maluszynska J: Chromosomal rearrangement in autotetraploid plants of Arabidopsis thaliana . Hereditas 133: 255-261 (2001).
176. Weiss-Schneeweiss H, Schneeweiss GM, Stuessy TF, Mabuchi T, Park JM, et al: Chromosomal stasis in diploids contrasts with genome restructuring in auto-and allopolyploid taxa of Hepatica (Ranunculaceae). New Phytol 174: 669-682 (2007).
177. Wendel J, Flagel L, Adams K: Jeans, genes, and genomes: cotton as a model for studying polyploidy, in Soltis PS, Soltis DE (eds): Polyploidy and Genome Evolution, pp 181-207 (Springer, Berlin Heidelberg 2012).
178. Wendel JF: Genome evolution in polyploids. Plant Mol Biol 42: 225-249 (2000).
179. Wendel JF, Cronn RC: Polyploidy and the evolutionary history of cotton. Adv Agron 78: 139-186 (2003).
180. Widmer A, Baltisberger M: Molecular evidence for allopolyploid speciation and single origin of the narrow endemic Draba ladina (Brassicaceae). Am J Bot 86: 1282-1289 (1999).
181. Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH: The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci USA 106: 13875-13879 (2009).
182. Xiong Z, Gaeta RT, Pires JC: Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus . Proc Natl Acad Sci USA 108: 7908-7913 (2011).
183. Xu Y, Zhao Q, Mei S, Wang J: Genomic and transcriptomic alterations following hybridisation and genome doubling in trigenomic allohexaploid Brassica carinata × Brassica rapa . Plant Biol 14: 734-744 (2012).
184. Xu Y, Xu H, Wu X, Fang X, Wang J: Genetic changes following hybridization and genome doubling in synthetic Brassica napus . Biochem Genet 50: 616-624 (2012).
185. Yaakov B, Kashkush K: Massive alterations of the methylation patterns around DNA transposons in the first four generations of a newly formed wheat allohexaploid. Genome 54: 42-49 (2011).
186. Yang X, Ye CY, Cheng ZM, Tschaplinski T, Wullschleger S, et al: Genomic aspects of research involving polyploid plants. Plant Cell Tiss Org 104: 387-397 (2011).
187. Yu Z, Haberer G, Matthes M, Rattei T, Mayer KFX, et al: Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana . Proc Natl Acad Sci USA 107: 17809-17814 (2010).
188. Zhang LQ, Liu DC, Zheng YL, Yan ZH, Dai SF, et al: Frequent occurrence of unreduced gametes in Triticum turgidum-Aegilops tauschii hybrids. Euphytica 172: 285-294 (2010).
189. Zhao N, Zhu B, Li M, Wang L, Xu L, et al: Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat. Genetics 188: 499-510 (2011).
190. Zhou R, Moshgabadi N, Adams KL: Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids. Proc Natl Acad Sci USA 108: 16122-16127 (2011).
191. Zou J, Fu D, Gong H, Qian W, Xia W, et al: De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa . Plant J 68: 212-224 (2011).