Mechanisms of chromosome rearrangements

Plant Genome Diversity

Volumn 2, Issue , 2013, Pages 137-147

  Lysák, Martin A ^a   Schubert, Ingo ^b  

^a MASARYK UNIVERSITY   (Czech Republic)

^b LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84930690686     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-1160-4_9     Document Type: Chapter

References (73)

1. Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C, Salse J (2010) Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci 15:479-487
2. Cenci A, Combes M-C, Lashermes P (2010) Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome. Mol Genet Genomics 283:493-501
3. Cohen S, Houben A, Segal D (2008) Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants. Plant J 53:1027-1034
4. Cremonini R (2005) Low chromosome number angiosperms. Caryologia 58:403-409
5. Darlington CD (1937) Recent advances in cytology. J. & A. Churchill, London
6. Datson PM, Murray BG (2006) Ribosomal DNA locus evolution in Nemesia: transposition rather than structural rearrangement as the key mechanism? Chromosome Res 14:845-857
7. Delprat A, Negre B, Puig M, Ruiz A (2009) The transposon Galileo generates natural chromosomal inversions in Drosophila by ectopic recombination. PLoS One 4(11):e7883. doi:10.1371/journal.pone.0007883
8. Dubcovsky J, Dvorák J (1995) Ribosomal RNA multigene loci: nomads of the Triticeae genomes. Genetics 140:1367-1377
9. Fawcett JA, Van de Peer Y, Maere S (2013) Significance and biological consequences of polyploidization in land plants. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 277-293
10. 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
11. Gaut BS, Wright SI, Rizzon C, Dvorák J, Anderson LK (2007) Recombination: an underappreciated factor in the evolution of plant genomes. Nat Rev Genet 8:77-84
12. Greilhuber J, Borsch T, Muller K, Worberg A, Porembski S, Barthlott W (2006) Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biol 8:770-777
13. Griffiths AJF, Gelbart WM, Lewontin RC (2007) Introduction to genetic analysis. W. H. Freeman, New York
14. Gu W, Zhang F, Lupski JR (2008) Mechanisms for human genomic rearrangements. Pathogenetics 1:4
15. Hall KJ, Parker JS (1995) Stable chromosome fission associated with rDNA mobility. Chromosome Res 3:417-422
16. Han F, Gao Z, Birchler JA (2009a) Reactivation of an inactive centromere reveals epigenetic and structural components for centromere specification in maize. Plant Cell 21:1929-1939
17. Han Y, Zhang Z, Liu C, Liu J, Huang S, Jiang J, Jin W (2009b) Centromere repositioning in cucurbit species: implication of the genomic impact from centromere activation and inactivation. Proc Natl Acad Sci USA 106:14937-14941
18. Imai HT (1991) Mutability of constitutive heterochromatin (C bands) during eukaryotic chromosomal evolution and their cytological meaning. Jpn J Genet 66:635-661
19. International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763-768
20. Jaillon O, Aury J-M, Wincker P (2009) "Changing by doubling", the impact of whole genome duplications in the evolution of eukaryotes. C R Biol 332:241-253
21. Jones K (1998) Robertsonian fusion and centric fission in karyotype evolution of higher plants. Bot Rev 64:273-289
22. Khandelwal S (1990) Chromosome evolution in the genus Ophioglossum L. Bot J Linn Soc 102:205-217
23. Leitch IJ, Leitch AR (2013) Genome size diversity and evolution in land plants. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 307-322
24. Levin DA (2002) The role of chromosomal change in plant evolution. Oxford University Press, New York
25. Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo HY, Huo N, Lazo G, Ma Y, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorák J (2009) Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc Natl Acad Sci USA 106:15780-15785
26. Lysák MA, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I (2006) Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc Natl Acad Sci USA 103:5224-5229
27. Mandáková T, Joly S, Krzywinski M, Mummenhoff K, Lysák MA (2010a) Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell 22:2277-2290
28. Mandáková T, Heenan PB, Lysák MA (2010b) Island species radiation and karyotypic stasis in Pachycladon allopolyploids. BMC Evol Biol 10:367
29. McClintock B (1948) Mutable loci in maize. Carnegie Inst Wash Year Book, vol 47., pp 155-169
30. Murat F, Xu JH, Tannier E, Abrouk M, Guilhot N, Pont C, Messing J, Salse J (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res 20:1545-1557
31. Murata M, Yokota E, Shibata F, Kashihara K (2008) Functional analysis of the Arabidopsis centromere by T-DNA insertion-induced centromere breakage. Proc Natl Acad Sci USA 105:7511-7516
32. Nasuda S, Hudakova S, Schubert I, Houben A, Endo TR (2005) Stable barley chromosomes without centromeric repeats. Proc Natl Acad Sci USA 102:9842-9847
33. Navrátilová A, Koblízková A, Macas J (2008) Survey of extrachromosomal circular DNA derived from plant satellite repeats. BMC Plant Biol 8:90
34. Nicolas SD, Le Mignon G, Eber F, Coriton O, Monod H, Clouet V, Huteau V, Lostanlen A, Delourme R, Chalhoub B, Ryder CD, Chèvre AM, Jenczewski E (2007) Homeologous recombination plays a major role in chromosome rearrangements that occur during meiosis of Brassica napus haploids. Genetics 175:487-503
35. Page SL, Shin J-C, Han J-Y, Choo KH, Andy SLG (1996) Breakpoint diversity illustrates distinct mechanisms for Robertsonian translocation formation. Hum Mol Genet 5:1279-1288
36. Pellicer J, Fay MF, Leitch IJ (2010) The largest eukaryotic genome of them all. Bot J Linn Soc 164:10-15
37. Perry J, Nouri S, La P, Daniel A, Wu Z, Purvis-Smith S, Northrop E, Choo KH, Slater HR (2005) Molecular distinction between true centric fission and pericentric duplication-fission. Hum Genet 116:300-310
38. Piras FM, Nergadze SG, Magnani E, Bertoni L, Attolini C, Khoriauli L, Raimondi E, Giulotto E (2010) Uncoupling of satellite DNA and centromeric function in the genus Equus. PLoS Genet 6: e1000845
39. Pulletikurti V, Yu C, Zhang J, Peterson T, Weber DF (2009) Cytological evidence that alternative transposition by Ac elements causes reciprocal translocations and inversions in Zea mays L. Maydica 54:457-462
40. Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, Roote J, Ashburner M, Bergman CM (2007) Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol 5:e152
41. Raskina O, Belyayev A, Nevo E (2004) Quantum speciation in Aegilops: molecular cytogenetic evidence from rDNA cluster variability in natural populations. Proc Natl Acad Sci USA 101:14818-14823
42. Raskina O, Barber JC, Nevo E, Belyayev A (2008) Repetitive DNA and chromosomal rearrangements: speciation-related events in plant genomes. Cytogenet Genome Res 120:351-357
43. Rocchi M, Stanyon R, Archidiacono N (2009) Evolutionary new centromeres in primates. Prog Mol Subcell Biol 48:103-152
44. Runcie DE, Noor MAF (2009) Sequence signatures of a recent chromosomal rearrangement in Drosophila mojavensis. Genetica 136:5-11
45. Salse J, Bolot S, Throude M, Jouffe V, Piegu B, Quraishi UM, Calcagno T, Cooke R, Delseny M, Feuillet C (2008) Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 20:11-24
46. Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, Waugh R, Close TJ, Messing J, Feuillet C (2009) Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci USA 106:14908-14913
47. Schubert I (1992) Telomeric polymorphism in Vicia faba. Biol Zbl 111:164-168
48. Schubert I (2007) Chromosome evolution. Curr Opin Plant Biol 10:109-115
49. Schubert I, Lysák MA (2011) Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet 27:207-216
50. Schubert I, Rieger R (1985) A new mechanism for altering chromosome number during karyotype evolution. Theor Appl Genet 70:213-221
51. Schubert I, Wobus U (1985) In situ hybridization confirms jumping nucleolus organizing regions in Allium. Chromosoma 92:143-148
52. Schubert I, Rieger R, Michaelis A (1988) On the toleration of duplications and deletions by the Vicia faba genome. Theor Appl Genet 76:64-70
53. Schubert I, Rieger R, Fuchs J (1995) Alteration of basic chromosome number by fusion-fission cycles. Genome 38:1289-1292
54. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng CF, Sankoff D, dePamphilis CW, Wall PK, Soltis PS (2009) Polyploidy and angiosperm diversification. Am J Bot 96:336-348
55. Stebbins GL (1971) Chromosomal evolution in higher plants. Edward Arnold, London
56. Stimpson KM, Sullivan BA (2010) Epigenomics of centromere assembly and function. Curr Opin Cell Biol 22:1-9
57. Sullivan BA, Jenkins LS, Karson EM, Leana-Cox J, Schwartz S (1996) Evidence for structural heterogeneity from molecular cytogenetic analysis of dicentric Robertsonian translocations. Am J Hum Genet 59:167-175
58. Thiel T, Graner A, Waugh R, Grosse I, Close TJ, Stein N (2009) Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. BMC Evol Biol 9:209
59. Thomas BC, Pedersen B, FreelingM(2006) Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 16:934-946
60. Tsujimoto H, Usami N, Hasegawa K, Yamada T, Nagaki K, Sasakuma T (1999) De novo synthesis of telomere sequences at the healed breakpoints of wheat deletion chromosomes. Mol Gen Genet 262:851-856
61. Udall JA, Quijada PA, Osborn TC (2005) Detection of chromosomal rearrangements derived from homologous recombination in four mapping populations of Brassica napus L. Genetics 169:967-979
62. Uhl CH (1978) Chromosomes of Mexican Sedum II. Section Pachysedum. Rhodora 80:491-512
63. Van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K (2009) The flowering world: A tale of duplications. Trends Plant Sci 14:680-688
64. Vanzela ALL, Guerra M, Luceno M (1996) Rhynchospora tenuis Link (Cyperaceae), a species with the lowest number of holocentric chromosomes (n = 2). Cytobios 88:219-228
65. Ventura M, Mudge JM, Palumbo V, Burn S, Blennow E, Pierluigi M, Giorda R, Zuffardi O, Archidiacono N, Jackson MS, Rocchi M (2003) Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25. Genome Res 13: 2059-2068
66. Ventura M, Antonacci F, Cardone MF, Stanyon R, D'Addabbo P, Cellamare A, Sprague LJ, Eichler EE, Archidiacono N, Rocchi M (2007) Evolutionary formation of new centromeres in macaque. Science 316:243-246
67. Voullaire LE, Slater HR, Petrovic V, Choo KH (1993) A functional marker centromere with no detectable alpha-satellite, satellite III, or CENP-B protein: activation of a latent centromere? Am J Hum Genet 52:1153-1163
68. Wei F, Coe E, Nelson W, Bharti AK, Engler F, Butler E, Kim H, Goicoechea JL, Chen M, Lee S, Fuks G, Sanchez-Villeda H, Schroeder S, Fang Z, McMullen M, Davis G, Bowers JE, Paterson AH, Schaeffer M, Gardiner J, Cone K, Messing J, Soderlund C, Wing RA (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3:e123
69. Weil CF (2009) Too many ends: aberrant transposition. Genes Dev 23:1032-1036
70. Wolfe KH (2001) Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2:333-341
71. Yang L, Bennetzen JL (2009) Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci USA 106:19922-19927
72. Yu S, Graf WD (2010) Telomere capture as a frequent mechanism for stabilization of the terminal chromosomal deletion associated with inverted duplication. Cytogenet Genome Res 129:265-274
73. Zhang J, Yu C, Pulletikurti V, Lamb J, Danilova T, Weber DF, Birchler J, Peterson T (2009) Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize. Genes Dev 23:755-765.