Duplications and turnover in plant genomes

Plant Genome Diversity

Volumn 1, Issue , 2014, Pages 155-169

  Barker, Michael S ^a   Baute, Gregory J ^b   Liu, Shao Lun ^b  

^a University of Arizona   (United States)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84930703425     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-1130-7_11     Document Type: Chapter

References (108)

1. Adams KL, Cronn R, Percifield R, Wendel J (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci U S A 100:4649-4654
2. Ameline-Torregrosa C, Wang B-B, O'Bleness MS, Deshpande S, Zhu H, Roe B, Young ND, Cannon SB (2008) Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol 146:5-21
3. Banks JA et al (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332:960-963
4. Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW, Knapp SJ, Rieseberg LH (2008) Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol Biol Evol 25:2445-2455
5. Barker MS, Vogel H, Schranz ME (2009) Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. Genome Biol Evol 1:391-399
6. Bekaert M, Edger PP, Pires JC, Conant GC (2011) Two phase resolution of polyploidy in Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Plant Cell 23:1719-1728
7. Belling J, Blakeslee AF (1924) The configurations and sizes of the chromosomes in trivalents of 25-chromosome Daturas. Proc Natl Acad Sci U S A 10:116-120
8. Birchler JA, Veitia RA (2007) The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19:395-402
9. Birchler JA, Bhadra MP, Auger DL (2001) Dosage-dependent gene regulation in multicellular eukaryotes: implications for dosage compensation, aneuploid syndromes, and quantitative traits. Dev Biol 234:275-288
10. Blakeslee AF (1921) Types of mutations and their possible significance in evolution. Am Nat 5:254-267
11. Blakeslee AF, Avery BT (1919) Mutations in the Jimson weed. J Hered 10:111-120
12. Blakeslee AF, Belling J, Farnham ME (1920) Chromosomal duplication and Mendelian phenomena in Datura mutants. Science 52:388-390
13. Blanc G, Wolfe KH (2004a) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-1678
14. Blanc G, Wolfe KH (2004b) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679-1691
15. Blanc G, Hokamp K, Wolfe KH (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13:137-144
16. Bowers JE, Chapman BA, Rong JK, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-438
17. Bradley D, Carpenter R, Sommer H, Hatley N, Coen E (1993) Complementary floral homeotic phenotypes result from opposite orientations of a transposon at the plena locus of Antirrhinum. Cell 72:85-95
18. Byun-McKay SA, Geeta R (2007) Protein subcellular relocalization: A new perspective on the origin of novel genes. Trends Ecol Evol 22:338-344
19. Byun-McKay SA, Geeta R, Duggan R, Carroll B, McKay SJ (2009) Missing the subcellular target: A mechanism of eukaryotic gene evolution. In: Pontarotti P (ed) Evolutionary biology: concept, modeling, and application. Springer, Berlin/Heidelberg/New York, pp 175-183
20. Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4:10
21. Casneuf T, De Bolt S, Raes J, Maere S, Van de Peer Y (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol 7:R13
22. Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N, Springer NM, Wendel J (2009) Reciprocal silencing, transcriptional bias and functional divergence of homoeologs in polyploid cotton (Gossypium). Genetics 182:503-517
23. Cifuentes M, Eber F, Lucas M-O, Lode M, Chèvre A-M, Jenczewski E (2010) Repeated polyploidy drove different levels of crossover suppression between homoeologous chromosomes in Brassica napus allohaploids. Plant Cell 22:2265-2276
24. Coen ES, Meyerowitz EM (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353:31-37
25. Conant GC, Wolfe KH (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9:938-950
26. Cronn RC, Small RL, Haselkorn T, Wendel J (2002) Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Am J Bot 89:707-725
27. Cui LY, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA, Ma H, dePamphilis CW (2006) Widespread genome duplications throughout the history of flowering plants. Genome Res 16:738-749
28. Des Marais DL, Rausher MD (2008) Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454:762-765
29. Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS, Wendel JF (2008) Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet 42:443-461
30. Duarte JM, Cui L, Wall PK, Zhang Q, Zhang X, Leebens-Mack J, Ma H, Altman N, dePamphilis CW (2006) Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol Biol Evol 23:467-478
31. Edger PP, Pires JC (2009) Gene and genome duplications: The impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res 17:699-717
32. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545
33. Freeling M (2009) Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu Rev Plant Biol 60:433-453
34. Freeling M, Thomas BC (2006) Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 16:805-814
35. Freeling M, Lyons E, Pederson B, Alam M, Ming R, Lisch D (2008) Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res 18:1924-1937
36. Ganko EW, Meyers BC, Vision TJ (2007) Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol 24:2298-2309
37. Haas BJ et al (2005) Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol 3:7
38. Haberer G, Hindemitt T, Meyers BC, Mayer KFX (2004) Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol 136:3009-3022
39. Hahn MW (2009) Distinguishing among evolutionary models for the maintenance of gene duplicates. J Hered 100:605-617
40. Haldane JBS (1933) The part played by recurrent mutation in evolution. Am Nat 67:5-9
41. Hanikenne M, Talke IN, Haydon MJ, Lanz C, Nolte A, Motte P, Kroymann J, Weigel D, Kramer U (2008) Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4. Nature 453:391-395
42. Harland SC (1936) The genetical conception of the species. Camb Philos Soc Biol Rev 11:83-112
43. Hiller LDW et al (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716
44. Hoen DR, Park KC, Elrouby N, Yu Z, Mohabir N, Cowan RK, Bureau TE (2006) Transposon-mediated expansion and diversification of a family of ULP-like genes. Mol Biol Evol 23:1254-1268
45. Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proc R Soc Lond B Biol Sci 256:119-124
46. Innan H, Kondrashov F (2010) The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11:97-108
47. Jaillon O et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467
48. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569-573
49. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderball AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Llang H, 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 473:97-100
50. Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res 15:1292-1297
51. Kawabe A, Fujimoto R, Charlesworth D (2007) High diversity due to balancing selection in the promoter region of the Medea gene in Arabidopsis lyrata. Curr Biol 17:1885-1889
52. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
53. Koh J, Soltis PS, Soltis DE (2010) Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae). BMC Genomics 11:97
54. Leitch IJ, Soltis DE, Soltis PS, Bennett MD (2005) Evolution of DNA amounts across land plants (Embryophyta). Ann Bot 95:207-217
55. Li Z, Zhang H, Ge S, Gu X, Gao G, Luo J (2009) Expression pattern divergence of duplicated gene in rice. BMC Bioinformatics 10:S8
56. Liang H, Plazonic KR, Chen J, Li WH, Fernández A (2008) Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. PLoS Genet 4:e11
57. 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
58. Lim KY, Soltis DE, Soltis PS, Tate J, Matyasek R, Srubarova H, Kovarik A, Pires JC, Xiong Z, Leitch AR (2008) Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). PLoS One 3:e3353
59. Liu S-L, Adams KL (2010) Dramatic change in function and expression pattern of a gene duplicated by polyploidy created a paternal effect gene in the Brassicaceae. Mol Biol Evol 27:2817-2828
60. Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF (2001) Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44:321-330
61. Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, Osborn T (2006) Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus. Plant Physiol 140:336-348
62. Lynch M (2007) The origins of genome architecture. Sinnauer, Sunderland
63. Lynch M, Conery JS (2003) The evolutionary demography of duplicate genes. J Struct Funct Genomics 3:35-44
64. Lynch M, Force AG (2000) The origin of interspecific genomic incompatibility via gene duplication. Am Nat 156:590-605
65. Lysak 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 U S A 103:5224-5229
66. Maere S, De Bodt S, Raes J, Casneuf T, Montagu M, Kuiper M, Van de Peer Y (2005) Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci U S A 102:5454-5459
67. Mandáková T, Joly S, Krzywinksi M, Mummenhoff K, Lysak MA (2010) Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell 22:2277-2290
68. MatsunoM, Compagnon V, Schoch GA, Schmitt M, Debayle D, Bassard J-E, Pollet B, Hehn A, Heintz D, Ullmann P, Lapierre C, Bernier F, Ehlting J, Werck-Reichhart D (2009) Evolution of a novel phenolic pathway for pollen development. Science 325:1688-1692
69. Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, Otto SP (2011) Recently formed polyploid plants diversify at lower rates. Science 333:1257
70. Mena M, Ambrose BA, Meeley RB, Briggs SP, YanofskyMF, Schmidt RJ (1996) Diversification of C function activity in maize flower development. Science 274:1537-1540
71. Miyake T, Takebayashi N, Wolf DE (2009) Possible diversifying selection in the imprinted gene, MEDEA, in Arabidopsis. Mol Biol Evol 26:843-857
72. Ohno S (1970) Evolution by gene duplication. Springer, Berlin/ Heidelberg/New York
73. Ohta T (1987) Simulating evolution by gene duplication. Genetics 115:207-213
74. Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, Ray A, van der Winden J, Matzke M, Matzke AJM (2003) Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol 132:1382-1390
75. Pfeil BE, Schlueter JA, Shoemaker RC, Doyle JJ (2005) Placing paleopolyploidy in relation to taxon divergence: A phylogenetic analysis in legumes using 39 gene families. Syst Biol 54:441-454
76. Rizzon C, Ponger L, Gaut BS (2006) Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol 2:e115
77. Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, Waugh R, Close TJ, Messing J, Feuillet C (2009) Reconstruction of monocotyledonous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci U S A 106:14908-14913
78. Sankoff D, Zheng C, Zhu Q (2010) The collapse of gene complement following whole genome duplication. BMC Genomics 11:313
79. Schmutz J et al (2010) Genome sequence of the paleopolyploid soybean. Nature 463:178-183
80. Schranz ME, Edger PP, Pires JC, van Dam N, Wheat CW (2011) Comparative genomics in the Brassicales: ancient genome duplications, glucosinolate diversification and Pierinae herbivore radiation. In: Edwards D, Batley J, Parkin I, Kole C (eds) Oilseeds: genetics, genomics, and breeding of oilseed brassicas. Science, Boca Raton
81. Schuermann D, Molinier J, Fritsch O, Hohn B (2005) The dual nature of homologous recombination in plants. Trends Genet 21:172-181
82. Sémon M, Wolfe KH (2007) Consequences of genome duplication. Curr Opin Genet Dev 17:505-512
83. Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, Noyes RD, Paterson AH, Wing RA, Wilkind TA, Wendel J (2003) Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol Biol Evol 20:633-643
84. Shi T, Huang H, Barker MS (2010) Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Ann Bot 106:497-504
85. Soltis DE, Soltis PS, Pires JC, Kovarik A, Tate JA, Mavrodiev E (2004) Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic and genetic comparisons. Biol J Linn Soc 82:485-501
86. Spillane C, Schmid KJ, Laoueillé-Duprat S, Pien S, Escobar-Restrepo J-M, Baroux C, Gagliardini V, Page DR, Wolfe KH, Gossniklaus U (2007) Positive Darwinian selection at the imprinted MEDEA locus in plants. Nature 448:349-352
87. Stebbins GL (1950) Variation and evolution in plants. Columbia University Press, New York
88. Stebbins GL (1971) Chromosomal evolution in higher plants. Addison-Wesley, Reading
89. Stephens SG (1951) Possible significance of duplication in evolution. Adv Genet 4:247-265
90. Tang HB, Bowers JE, Wang XY, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. Science 320:486-488
91. 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
92. ThroudeM, Bolot S, BosioM, Pont C, Sarda X, QuraishiUM, Bourgis F, Lessard P, Rogowsky P, Ghesquiere A, Murigneux A, Charmet G, Perez P, Salse J (2008) Structure and expression analysis of rice paleo duplications. Nucleic Acids Res 37:1248-1259
93. Tian C, Xiong Y, Liu T, Sun S, Chan L, ChenM(2005) Evidence for an ancient whole-genome duplication event in rice and other cereals. Acta Genet Sin 32:519-527
94. Tuskan GA et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596-1604
95. Veitia RA (2002) Exploring the etiology of haploinsuffinciency. Bioessays 24:175-184
96. Veitia RA (2003) Nonlinear effects in macromolecular assembly and dosage sensitivity. J Theor Biol 220:19-25
97. Veitia RA (2005) Paralogs in polyploids: one for all and all for one? Plant Cell 17:4-11
98. Vision TJ, Brown DG, Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290:2114-2117
99. Wagner WH (1970) Biosystematics and evolutionary noise. Taxon 19:146-151
100. Walsh JB (1995) How often do duplicated genes evolve new functions? Genetics 139:421-428
101. Wang X, Shi X, Hao B, Ge S, Luo J (2005) Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 165:937-946
102. Wolfe KH (2001) Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2:333-341
103. Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH (2009) The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci U S A 106:13875-13879
104. Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M (2010) Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biol 8(6):e1000409
105. Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319:1527-1530
106. Xiong Z, Gaeta RT, Pires JC (2011) Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc Natl Acad Sci U S A 108:7908-7913
107. Yanofsky MF, Ma H, Bowman JL, Drews GN, Feldmann KA, Meyerowitz EM (1990) The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346:35-39
108. Zou C, Lehti-Shiu MD, Thomashow M, Shiu S-H (2009) Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana. PLoS Genet 5:e1000581