Evolutionary implications of genome and karyotype restructuring in nicotiana tabacum L

Polyploidy and Genome Evolution

Volumn 9783642314421, Issue , 2012, Pages 209-224

  Kovarik, Ales ^a   Renny Byfield, Simon ^b   Grandbastien, Marie Angèle ^c   Leitch, Andrew ^b  

^a INSTITUTE OF BIOPHYSICS   (Czech Republic)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^c INSTITUT JEAN PIERRE BOURGIN   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84949178645     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-642-31442-1_11     Document Type: Chapter

References (82)

1. Adams KL, Wendel JF (2005) Allele-specific, bidirectional silencing of an alcohol dehydrogenase gene in different organs of interspecific diploid cotton hybrids. Genetics 171:2139-2142
2. Bejarano ER, Khashoggi A, Witty M, Lichtenstein C (1996) Integration of multiple repeats of geminiviral DNA into the nuclear genome of tobacco during evolution. Proc Nat Acad Sci USA 93:759-764
3. Birchler JA, Veitia RA (2010) The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol 186:54-62
4. Buggs RJ, Doust AN, Tate JA, Koh J, Soltis K, Feltus FA, Paterson AH, Soltis PS, Soltis DE (2009) Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity 103:73-81
5. Buggs RJA, Chamala S, Wu W, Tate JA, Schnable PS, Soltis DE, Soltis PS, Barbazuk WB (2012) Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Curr Biol 22:248-252
6. Burk LG (1973) Partial self-fertility in a theoretical amphiploid progenitor of N. tabacum. J Hered 64:348-350
7. Butlin RK (1993) Species evolution-The role of chromosome change-King, M. Nature 366:27
8. Chakrabarti M, Meekins KM, Gavilano LB, Siminszky B (2007) Inactivation of the cytochrome P450 gene CYP82E2 by degenerative mutations was a key event in the evolution of the alkaloid profile of modern tobacco. New Phytol 175:565-574
9. Chase MW, Knapp S, Cox AV, Clarkson JJ, Butsko Y, Joseph J, Savolainen V, Parokonny AS (2003) Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae). Ann Bot 92:107-127
10. Chester M, Gallagher JP, Symonds VV, Cruz da Silva AV, Mavrodiev EV, Leitch AR, Soltis PS and Soltis DE (2012) Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proceedings of the National Academy of Sciences of the United States of America, 109:1176-1181
11. Chester M, Sykorova E, Fajkus J, Leitch AR (2010) Single integration and spread of a Copia-like sequence nested in rDNA intergenic spacers of Allium cernuum (Alliaceae). Cytogenet Genome Res 129:35-46
12. Clarkson JJ, Kelly LJ, Leitch AR, Knapp S, Chase MW (2010) Nuclear glutamine synthetase evolution in Nicotiana: phylogenetics and the origins of allotetraploid and homoploid (diploid) hybrids. Mol Phylogenet Evol 55:99-112
13. Clarkson JJ, Lim KY, Kovarik A, Chase MW, Knapp S, Leitch AR (2005) Long-term genome diploidization in allopolyploid Nicotiana section Repandae (Solanaceae). New Phytol 168:241-252
14. Colot V, Goyon C, Faugeron G, Rossignol JL (1995) Methylation of repeated DNA sequences and genome stability in Ascobolus immersus. Can J Bot-Rev Canadienne De Botanique 73:S221-S225
15. Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS, Wendel JF (2008) Evolutionary genetics of genome merger and doubling in plants. Ann Rev Genet 443-461
16. Feder JL, Nosil P (2009) Chromosomal inversions and species differences: when are geens affecting adaptive divergence and reproductive isolation expected to reside within inversions? Evolution 63:3061-3075
17. Feldman M, Levy AA (2009) Genome evolution in allopolyploid wheat-A revolutionary reprogramming followed by gradual changes. J Genet Genomics 36:511-518
18. Fulnecek J, Lim KY, Leitch AR, Kovarik A, Matyasek R (2002) Evolution and structure of 5S rDNA loci in allotetraploid Nicotiana tabacum and its putative parental species. Heredity 88:19-25
19. Fulnecek J, Matyasek R, Kovarik A (2009) 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
20. Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC (2007) Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19:3403-3417
21. Gazdova B, Siroky J, Fajkus J, Brzobohaty B, Kenton A, Parokonny A, Heslop-Harrison JS, Palme K, Bezdek M (1995) Characterization of a new family of tobacco highly repetitive DNA, GRS, specific for the Nicotiana tomentosiformis genomic component. Chromosome Res 3:245-254
22. Gerstel DU, Burns JA (1967) Phenotypic and chromosomal abnormalities associated with the introduction of heterochromatin from Nicotiana otophora into N. tabacum. Genetics 56:483-502
23. Gill BS (1991) Nucleocytoplasmic interaction (NCI) hypothesis of genome evolution and speciation in polyploid plants. In: Sasakuma T, KinoshitaT (ed.) Proceedings of the Kihara memorial international symposium on cytoplasmic engineering in wheat, Kihara Memorial Foundation, Yokohama, Japan, pp 48-53
24. Goodspeed TH (1954) The genus Nicotiana Massachusetts. Chronica Botanica Company, USA.
25. Grandbastien M, Audeon C, Bonnivard E, Casacuberta JM, Chalhoub B, Costa APP, Le QH, Melayah D, Petit M, Poncet C, Tam SM, Van Sluys MA, Mhiri C (2005) Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenetic Genome Res 110:229-241
26. Heslop-Harrison JS, Schwarzacher T (2011) Organisation of the plant genome in chromosomes. Plant J 66:18-33
27. Intrieri MC, Muleo R, Buiatti M (2008) Phytochrome A as a functional marker of phyletic relationships in Nicotiana genus. Biol Plant 52:36-41
28. Jakowitsch J, Mette MF, van der Winden J, Matzke MA, Matzke AJM (1999) Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants. Proc Nat Acad Sci USA 96:13241-13246
29. Jakowitsch J, Papp I, Matzke MA, Matzke AJM (1998) Identification of a new family of highly repetitive DNA, NTS9, that is located predominantly on the S9 chromosome of tobacco. Chromosome Res 6:649-659
30. Jiao YN, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang HY, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473:97-113
31. Kelly LJ, Leitch AR, Clarkson JJ, Hunter RB, Knapp S, Chase MW (2010) Intragenic recombination events and evidence for hybrid speciation in Nicotiana (Solanaceae). Mol Biol Evol 27:781-799
32. Kenton A, Parokonny AS, Gleba YY, Bennett MD (1993) Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics. Mol Gen Genet 240:159-169
33. King M (1993) Species evolution the role of chromosome change. Cambridge University Press, Cambridge.
34. Knapp S, Chase MW, Clarkson JJ (2004) Nomenclatural changes and a new sectional classification in Nicotiana (Solanaceae). Taxon 53:73-82
35. Kobayashi T (2011) Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast. Cell Mol Life Sci 68:1395-1403
36. Koukalova B, Moraes AP, Renny-Byfield S, Matyasek R, Leitch AR, Kovarik A (2010) Fall and rise of satellite repeats in allopolyploids of Nicotiana over c. 5 million years. New Phytol 186:148-160
37. Koukalova B, Reich J, Matyasek R, Kuhrova V, Bezdek M (1989) A BamHI family of highly repeated DNA sequecnes of Nicotiana tabacum. Theor Appl Genet 78:77-80
38. Kovarik A, Dadejova M, Lim K, Chase M, JJ C, Knapp S, Leitch A (2008) Evolution of rDNA in Nicotiana allopolyploids: a potential link between rDNA homogenization and epigentics. Ann Bot 101:815-823
39. Kovarik A, Fajkus J, Koukalova B, Bezdek M (1996) Species-specific evolution of telomeric and rDNA repeats in the tobacco composite genome. Theor Appl Genet 92:1108-1111
40. Kronenberger J, Lepingle A, Caboche M, Vaucheret H (1993) Cloning and expession of distinct nitrite reductases in tobacco-leaves and roots. Mol Gen Genet 236:203-208
41. Le Comber SC, Ainouche ML, Kovarik A, Leitch AR (2010) Making a functional diploid: from polysomic to disomic inheritance. New Phytol 186:113-122
42. Leitch AR, Lim KY, Skalicka K, Kovarik A (2006) Nuclear cytoplasmic interaction hypothesis and the role of translocations in Nicotiana allopolyploids. In: Cigna AAD, M. Yerevan (eds.) Radiation risk estimates in normal and emergency situations book series: NATO security through science series B: Physics and Biophysics (ARMENIA) pp 319-326
43. Leitch IJ, Bennett MD (2004) Genome downsizing in polyploid plants. Biol J Linn Soc 82:651-663
44. Leitch IJ, Hanson L, Lim KY, Kovarik A, Chase MW, Clarkson JJ, Leitch AR (2008) The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Ann Bot 101:805-814
45. Lim KY, Kovarik A, Matyasek R, Bezdek M, Lichtenstein CP, Leitch AR (2000a) Gene conversion of ribosomal DNA in Nicotiana tabacum is associated with undermethylated, decondensed and probably active gene units. Chromosoma 109:161-172
46. Lim KY, Kovarik A, Matyasek R, Chase MW, Clarkson JJ, Grandbastien MA, Leitch AR (2007) Sequence of events leading to near-complete genome turnover in allopolyploid Nicotiana within five million years. New Phytol 175:756-763
47. Lim KY, Matyasek R, Kovarik A, Leitch AR (2004a) Genome evolution in allotetraploid Nicotiana. Biol J Linn Soc 82:599-606
48. Lim KY, Matyasek R, Lichtenstein CP, Leitch AR (2000b) Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Chromosoma 109:245-258
49. Lim KY, Skalicka K, Koukalova B, Volkov RA, Matyasek R, Hemleben V, Leitch AR, Kovarik A (2004b) Dynamic changes in the distribution of a satellite homologous to intergenic 26-18S rDNA spacer in the evolution of Nicotiana. Genetics 166:1935-1946
50. Lim KY, Soltis DE, Soltis PS, Tate J, Matyasek R, Srubarova H, Kovarik A, Pires JC, Xiong ZY, Leitch AR (2008) Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). Plos One, 3
51. Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF (2002) Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44:321-330
52. Lynch M, O'Hely M, Walsh B, Force A (2001) The probability of preservation of a newly arisen gene duplicate. Genetics 159:1789-1804
53. Mandakova T, Joly S, Krzywinski M, Mummenhoff K, Lysak MA (2010) Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell 22:2277-2290
54. Matassi G, Melis R, Macaya G, Bernardi G (1991) Compositional bimodality of the nuclear genome of tobacco. Nucleic Acids Res 19:5561-5567
55. Matyasek R, Gazdova B, Fajkus J, Bezdek M (1997) NTRS, a new family of highly repetitive DNAs specific for the T1 chromosome of tobacco. Chromosoma 106:369-379
56. Matzke M, Gregor W, Mette MF, Aufsatz W, Kanno T, Jakowitsch J, Matzke AJM (2004) Endogenous paragretroviruses of polyploid Nicotiana tabacum and its diploid progenitors, N. sylvestris and N. tomentosiformis. Biol J Linn Soc 82:627-638
57. McCarthy EW (2010) The effect of molecular and spectral reflectance evolution on Nicotiana polyploids of different ages. In School of Biological and Chemical Sciences. London: Ph.D. thesis from Queen Mary University of London, p 259
58. McClintock B (1984) The significance of responses of the genome to challenge. Science 226:792-801
59. Melayah D, Bonnivard E, Chalhoub B, Audeon C, Grandbastien MA (2001) The mobility of the tobacco Tnt1 retrotransposon correlates with its transcriptional activation by fungal factors. Plant Journal, 28:159-168
60. Mestiri I, Chague V, Tanguy AM, Huneau C, Huteau V, Belcram H, Coriton O, Chalhoub B, Jahier J (2010) Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity. New Phytol 186:101-186
61. Moscone EA, Matzke MA, Matzke AJM (1996) The use of combined FISH/GISH in conjunction with DAPI counterstaining to identify chromosomes containing transgene inserts in amphidiploid tobacco. Chromosoma 105:231-236
62. Murad L, Bielawski JP, Matyasek R, Kovarik A, Nichols RA, Leitch AR, Lichtenstein CP (2004) The origin and evolution of Geminivirus-related DNA sequences in Nicotiana. Heredity 92:352-358
63. Murad L, Lim KY, Christopodulou V, Matyasek R, Lichtenstein CP, Kovarik A, Leitch AR (2002) The origin of tobacco's T genome is traced to a particular lineage within Nicotiana tomentosiformis (Solanaceae). Am J Bot 89:921-928
64. Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien MA, Ainouche M (2009) Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol 184:1003-1015
65. Petit M, Guidat C, Daniel J, Denis E, Montoriol E, Bui QT, Lim KY, Kovarik A, Leitch AR, Grandbastien MA, Mhiri C (2010) Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol 186:135-147
66. Petit M, Lim KY, Julio E, Poncet C, de Borne FD, Kovarik A, Leitch AR, Grandbastien MA, Mhiri C (2007) Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Mol Genet Genomics 278:1-15
67. Renny-Byfield S, Chester M, Kovarik A, Le Comber S, Grandbastien M, Deloger M, Nichols R, Macas J, Novak P, Chase M, Leitch A (2011) Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs Molecular Biology and Evolution 28:2843-2854
68. Renny-Byfield S, Kovarik A, Chester M, Nichols RA, Macas J, Novak P and Leitch AR (2012) Independent, rapid and targeted loss of highly repetitive DNA in natural and synthetic allopolyploids of Nicotiana tabacum. Plos One, 7:e36963
69. Riechers DE, Timko MP (1999) Structure and expression of the gene family encoding putrescine N-methyltransferase in Nicotiana tabacum: new clues to the evolutionary origin of cultivated tobacco. Plant Mol Biol 41:387-401
70. Rieseberg LH (1997) Hybrid origins of plant species. Annu Rev Ecol Syst 28:359-389
71. Schenke D, Sasabe M, Toyoda K, Inagaki Y, Shiraishi T, Ichinose Y (2003) Genomic structure of the NtPDR1 gene, harboring the two miniature inverted-repeat transposable elements, NtToya1 and NtStowaway101. Genes Genet Syst 78:409-418
72. Skalicka K, Lim KY, Matyasek R, Matzke M, Leitch AR, Kovarik A (2005) Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco. New Phytol 166:291-303
73. Soltis DE, Buggs RJA, Doyle JJ, Soltis PS (2010) What we still don't know about polyploidy. Taxon 59:1387-1403
74. Song KM, Lu P, Tang KL and Osborn TC (1995) Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proceedings of the National Academy of Sciences of the United States of America, 92:7719-7723
75. Sperisen C, Ryals J, Meins F (1991) Comparison of cloned genes provides evidence for intergenomic exchange of DNA in the evolution of a tobacco glucan endo-1, 3 betaglucosidase gene family. Proc Nat Acad Sci USA 88:1820-1824
76. Strasburg JL, Scotti-Saintagne C, Scotti I, Lai Z, Rieseberg LH (2009) Genomic patterns of adaptive divergence between chromosomally differentiated sunflower species. Mol Biol Evol 26:1341-1355
77. Szadkowski E, Eber F, Huteau V, Lode M, Coriton O, Jenczewski E and Chevre AM (2011) Polyploid formation pathways have an impact on genetic rearrangements in resynthesized Brassica napus. New Phytologist, 191:884-894
78. Takumi S, Ida M, Haisa Y, Ando S, Nakamura C (2002) Genomic structure and homoeologous relationship of the two alpha-subunit genes of a heterotrimeric GTP-binding protein in tobacco. Genome 45:626-633
79. Turner TL, Hahn MW (2010) Genomic islands of speciation or genomic islands and speciation? Mol Ecol 19:848-850
80. Vaucheret H, Vincentz M, Kronenberger J, Caboche M, Rouze P (1989) Molecular cloning and characterization of the 2 homologous genes coding for nitrate reductase in tobacco. Mol Gen Genet 216:10-15
81. Volkov RA, Borisjuk NV, Panchuk II, Schweizer D, Hemleben V (1999) Elimination and rearrangement of parental rDNA in the allotetraploid Nicotiana tabacum. Mol Biol Evol 16:311-320
82. Xiong ZY, Gaeta RT, Pires JC (2011) Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc Nat Acad Sci USA 108:7908-7913