Evolutionary dynamics of duplicated genes in plants

Molecular Phylogenetics and Evolution

Volumn 29, Issue 3, 2003, Pages 396-409

  Lawton Rauh, Amy ^a,b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

Author keywords

Evolutionary genomics; Gene duplication; Genome duplication; Polyploidy

Indexed keywords

EID: 0038032632     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.07.004     Document Type: Article

References (139)

1. Ahn, S., Tanksley, S.D., 1993. Comparative linkage maps of the rice and maize genomes. Proc. Natl. Acad. Sci. USA 90, 7980-7984.
2. Albert, V.A., Oppenheimer, D.G., Lindqvist, C., 2002. Pleiotropy, redundancy and the evolution of flowers. Trends Plant Sci. 7, 297-301.
3. Alvarez-Buylla, E.R., Pelaz, S., Liljegren, S.J., Gold, S.E., Burgeff, C., Ditta, G.S., Ribas De Pouplana, L., Martinez-Castilla, L., Yanofsky, M.F., 2000. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc. Natl. Acad. Sci. USA 97, 5328-5333.
4. Baldwin, B.G., 1997. Adaptive radiation of the Hawaiian silversword alliance: Congruence and conflict of phylogenetic evidence from molecular and non-molecular investigations. Cambridge University Press, Cambridge.
5. Baldwin, E.G., Kyhos, D.W., Dvorak, J., Carr, G.D., 1991. Chloroplast DNA evidence for the North American origin of the Hawaiian silversword alliance (Asteraceae). Proc. Natl. Acad. Sci. USA 88, 1840-1843.
6. Baldwin, B., Robichaux, R.H., 1995. Historical biogeography and ecology of the Hawaiian silversword alliance: new molecular phylogenetic perspectives. Smithsonian Institution Press, Washington, D.C.
7. Baldwin, B.G., Sanderson, M., 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc. Natl. Acad. Sci. USA 95, 9402-9406.
8. Barnes, S., 2002. Comparing Arabidopsis to other flowering plants. Curr. Opin. Plant Biol. 5, 128-133.
9. Barrier, M., Baldwin, B., Robichaux, R., Purugganan, M., 1999. Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications. Mol. Biol. Evol. 16, 1105-1113.
10. Barrier, M., Robichaux, R.H., Purugganan, M.D., 2001. Accelerated regulatory gene evolution in an adaptive radiation. Proc. Natl. Acad. Sci. USA 98, 10208-10213.
11. Baumel, A., Ainouche, M., Kalendar, R., Schulman, A.H., 2002. Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae). Mol. Biol. Evol. 19, 1218-1227.
12. Bennetzen, J.L., 2002. Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115, 29-36.
13. Bennetzen, J.L., Freeling, M., 1997. The unified grass genome: synergy in synteny. Gen. Res. 7, 301-306.
14. Bennetzen, J.L., Kellogg, E.A., 1997. Do plants have a one-way ticket to genomic obesity? Plant Cell 9, 1509-1514.
15. Blanc, G., Hokamp, K., Wolfe, K.H., 2003. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Gen. Res. 13, 137-144.
16. Brochmann, C., Elven, R., 1992. Ecological and genetic consequences of polyploidy in arctic Draba (Brassicaceae). Evol. Trends Plants 6, 111-124.
17. Brochmann, C., Xiang, Q.Y., Brunsfeld, S.J., Soltis, D.E., Soltis, P.S., 1998. Molecular evidence for polyploid origins in Saxifraga (Saxifragaceae): the narrow arctic endemic S.svalbardensis and its widespread allies. Am. J. Bot. 85, 135-143.
18. Brubaker, C.L., Paterson, A.H., Wendel, J.F., 1999. Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42, 184-203.
19. Carr, G.D., 1985. Monograph of the Hawaiian Madiinae (Asteraceae): Argyroxiphium, Dubautia, and Wilkesia. Allertonia 4, 1-123.
20. Charlesworth, D., Liu, F., Zhang, L., 1998. The evolution of the alcohol dehydrogenase gene family by loss of introns in plants of the genus Leavenworthia (Brassicaceae). Mol. Biol. Evol. 15, 52-559.
21. Clauss, M.J., Mitchell-Olds, T., 2003. Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history. Mol. Ecol. 12, 1287-1299.
22. Comai, L., 2000. Genetic and epigenetic interactions in allopolyploid plants. Plant Mol. Biol. 43, 387-399.
23. Comai, L., Tyagi, A., Winter, K., Holmes-Davis, R., Reynolds, S., Stevens, Y., Byers, B., 2000. Phenotypic instability and rapid genome silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12, 1551-1567.
24. Cook, L., Soltis, P.S., Brunsfeld, S.J., Soltis, D.E., 1998. Multiple independent formations of Tragopogon tetraploids (Asteraceae): evidence from RAPD markers. Mol. Ecol. 7, 1293-1302.
25. Cook, L., Soltis, P., 2000. Mating systems of diploid and allotetraploid populations of Tragopogon (Asteraceae). II. Artificial populations. Heredity 84, 410-415.
26. Cronn, R.C., Small, R.L., Wendel, J.F., 1999. Duplicated genes evolve independently after polyploid formation in cotton. Proc. Natl. Acad. Sci. USA 96, 14406-14411.
27. Dias, A.P., Braun, E.L., McMullen, M.D., Grotewold, E., 2003. Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication. Plant Phys. 131, 610-620.
28. Durbin, M.L., McCaig, B., Clegg, M.T., 2000. Molecular evolution of the chalcone synthase multigene family in the morning glory genome. Plant Mol. Biol. 42, 79-92.
29. Eckardt, N.A., 2001. A sense of self: the role of DNA sequence elimination in allopolyploidization. Plant Cell 13, 1699-1704.
30. Ferris, S.D., Whitt, G.S., 1977. Loss of duplicate gene expression after polyploidisation. Nature 265, 258-260.
31. Ferris, S.D., Whitt, G.S., 1979. Evolution of differential regulation of duplicate genes after polyploidization. J. Mol. Evol. 12, 267-317.
32. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.-L., Postlethwait, J., 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545.
33. Ford, V.S., Gottlieb, L.D., 1999. Molecular characterization of PgiC in a tetraploid plant and its diploid relatives. Evolution 53, 1060-1067.
34. Ford, V.S., Gottlieb, L.D., 2002. Single mutations silence PgiC2 genes in two very recent allotetraploid species of Clarkia. Evolution 56, 699-707.
35. Gaut, B.S., Doebley, J.F., 1997. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 94, 6809-6814.
36. Gaut, B.S., Le Thierry D'ennequin, M., 2000. Maize as a model for the evolution of plant nuclear genomes. Proc. Natl. Acad. Sci. USA 97, 7008-7015.
37. Gill, B.S., 1991. Nucleo-cytoplasmic interaction (NCI) hypothesis of genome evolution and speciation in polyploid plants. In: Sasakuma, T., Kinoshita, T. (Eds.), Proceedings of the Kihara Memorial International Symposium on Cytoplasmic Engineering in Wheat, Yokohoma, Japan, pp. 48-53.
38. Gilmour, S.J., Zarka, D.G., Stockinger, E.J., Salazar, M.P., Houghton, J.M., Thomashow, M.F., 1998. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 16, 433-442.
39. Gomez, M.I., Islam-Faridi, M.N., Zwick, M.S., Czeschin, D.G., Hart, G.E., Wing, R.A., Stelly, D.M., Price, H.J., 1998. Tetraploid nature of Sorghum bicolor (L.) Moench. J. Heredity 89, 188-190.
40. Gottlieb, L.D., Weeden, N.F., 1979. Gene duplication and phylogeny in Clarkia. Evolution 33, 1024-1039.
41. Gottlieb, L.D., Ford, V.S., 1996. Phylogenetic relationships among the sections of Clarkia (Onagraceae) inferred from the nucleotide sequences of PgiC. Syst. Bot. 20, 45-62.
42. Gottlieb, L.D., Ford, V.S., 1997. A recently silenced, duplicate PgiC locus in Clarkia. Mol. Biol. Evol. 14, 125-132.
43. Grant, V., 1981. Plant Speciation. Columbia University Press, New York.
44. Haake, V., Cook, D., Riechmann, J.L., Pineda, O., Thomashow, M.F., Zhang, J.Z., 2002. Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis. Plant Physiol. 130, 639-648.
45. Hileman, L.C., Baum, D.A., 2003. Why do paralogs persist? Molecular evolution of CYCLOIDEA and related floral symmetry genes in Antirrhineae (Veronicaceae). Mol. Biol. Evol. 20, 591-600.
46. Hilu, K.W., 1993. Polyploidy and the evolution of domesticated plants. Am. J. Bot. 80, 1494-1499.
47. Hughes, A.L., 1999. Adaptive Evolution of Genes and Genomes. Oxford University Press, Oxford.
48. Hughes, A.L., 2002. Adaptive evolution after gene duplication. Trends Genet. 18, 433-434.
49. Husband, B.C., Schemske, D.W., 2000. Ecological mechanisms of reproductive isolation between diploid and tetraploid Chamerion angustifolium. J. Ecol. 88, 689-701.
50. Jackson, R., 1976. Evolution and systematic significance of polyploidy. Ann. Rev. Ecol. Syst. 7, 209-234.
51. Johansen, B., Pedersen, L.B., Skipper, M., Frederiksen, S., 2002. MADS-box gene evolution - structure and transcription patterns. Mol. Phylogenet. Evol. 23, 458-480.
52. Kellogg, E.A., 1998. Relationships of cereal crops and other grasses. Proc. Natl. Acad. Sci. USA 95, 2005-2010.
53. Kempin, S., Savidge, B., Yanofsky, M.F., 1995. Molecular basis of the cauliflower phenotype in Arabidopsis. Science 267, 522-525.
54. Kliebenstein, D., Lambrix, V., Reichelt, M., Gershenzon, J., Mitchell-Olds, T., 2001. Gene duplication in the diversification of secondary metabolism: tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis. Plant Cell 13, 681-693.
55. Kramer, E.M., Dorit, R.L., Irish, V.F., 1998. Molecular evolution of genes controlling petal and stamen development: duplication and divergence within the APETALA3 and PISTILLATA MADS-box gene lineages. Genetics 149, 765-783.
56. Kramer, E.M., Di Stilio, V.S., Schluter, P.M., 2003. Complex patterns of gene duplication in the APETALA3 and PISTILLATA lineages of the Ranunculaceae. Int. J. Plant Sci. 164, 1-11.
57. Ku, H.M., Vision, T.J., Liu, J., Tanksley, S., 2000. Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by a selective gene loss creates a network of synteny. Proc. Natl. Acad. Sci. USA 97, 9121-9126.
58. Lagercrantz, U., 1998. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent recombinations. Genetics 150, 1217-1228.
59. Lagercrantz, U., Lydiate, D.J., 1996. Comparative genome mapping in Brassica. Genetics 144, 1903-1910.
60. Lawton-Rauh, A., Alvarez-Buylla, E.R., Purugganan, M.D., 2000. Molecular evolution of flower development. Trends Ecol. Evol. 15, 144-149.
61. Lawton-Rauh, A., Robichaux, R.H., Purugganan, M.D., 2003, Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae). Mol. Ecol. 12, 1301-1313.
62. Lee, H.S., Chen, Z.J., 2001. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. USA 98, 6753-6758.
63. Lee, J.M., Grant, D., Vallejos, C.E., Shoemaker, R.C., 2001. Genome organization in dicots. II. Arabidopsis as a 'bridging species' to resolve genome evolution events among legumes. Theor. Appl. Genet. 103, 765-773.
64. Leitch, I., Bennett, M., 1997. Polyploidy in angiosperms. Trends Plant Sci. 2, 470-476.
65. Lespinet, O., Wolf, Y.I., Koonin, E.V., Aravind, L., 2002. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12, 1048-1059.
66. Levin, D.A., 1983. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1-25.
67. Lewis, E.J., 1980. Chromosome pairing in tetraploid hybrids between Lolium perenne and L. multiflorum. Theor. Appl. Genet. 58, 137-143.
68. Liu, B., Brubaker, C.L., Mergeai, G., Cronn, R.C., Wendel, J.F., 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44, 321-330.
69. Liu, B., Wendel, J.F., 2003. Non-mendelian phenomena in allopolyploid genome evolution. Curr. Genomics 3, 1-17.
70. Love, A., Love, D., Pichi-Sermolli, R.E.G., 1977. Cytotaxonomical Atlas of Pteridophyta. Cramer, Vaduz, Germany.
71. Lumaret, R., 1988. Adaptive strategies and ploidy levels. Acta Aecologica 9, 83-93.
72. Lynch, M., 2002. Gene duplication and evolution. Science 297, 945-947.
73. Lynch, M., Conery, J.S., 2000. The Evolutionary Fate and Consequences of Duplicate Genes. Science 290, 1151-1155.
74. Lynch, M., Force, A., 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154, 459-473.
75. Madlung, A., Masuelli, R.W., Watson, B., Reynolds, S.H., Davison, J., Comai, L., 2002. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol. 129, 733-746.
76. Malaga-Trillo, E., Meyer, A., 2001. Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes. Am. Zool. 41, 676-686.
77. Masterson, J., 1994. Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science 264, 421-424.
78. Mathews, S., Sharrock, R.A., 1997. Phytochrome gene diversity. Plant Cell Environ. 20, 666-671.
79. McClintock, B., 1967. Genetic systems regulating gene expression during development. In: Control Mechanisms in Developmental Processes. Academic Press, New York.
80. Medina, J., Bargues, M., Terol, J., Perez-Alonso, M., Salinas, J., 1999. The Arabidopsis CBF gene family is composed of three genes encoding AP2 domain-containing proteins whose expression is regulated by low temperature but not by abscisic acid or dehydration. Plant Physiol. 119, 463-470.
81. Mena, M., Ambrose, B.A., Meeley, R.B., Briggs, S.P., Yanofsky, M.F., Schmidt, R.J., 1996. Diversification of C-function activity in maize flower development. Science 274, 1537-1539.
82. Mitchell-Olds, T., Clauss, M., 2002. Plant evolutionary genomics. Curr. Opin. Plant Biol. 5, 74-79.
83. Moore, G., Devos, K.M., Wang, Z., 1995. Grasses, line up and form a circle. Curr. Biol. 5, 737-739.
84. 2 genomes of cotton. Genome 41, 616-625.
85. Nadeau, J.H., Sankoff, D., 1997. Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics 147, 1259-1266.
86. Ng, M., Yanofsky, M.F., 2001. Function and evolution of the plant MADS-box gene family. Nat. Rev. Genet. 2, 186-195.
87. Ohno, S., 1970. Evolution by gene duplication. Springer-Verlag, New York.
88. Otto, S., Whitton, J., 2000. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401-437.
89. Ozkan, H., Levy, A., Feldman, M., 2001. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13, 1735-1747.
90. Osborn, T.C., Pires, J.C., Birchler, J.A., Auger, D.L., Chen, Z.J., Lee, H.-S., Comai, L., Madlung, A., Doerge, R.W., Colot, V., Martienssen, R.A., 2003. Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19, 141-147.
91. Paterson, A.H., Bowers, J.E., Burow, M.D., Draye, X., Elsik, C.G., Jiang, C.X., Katsar, C.S., Lan, T.H., Lin, Y.R., Ming, R., Wright, R.J., 2000. Comparative genomics of plant chromosomes. Plant Cell 12, 1523-1539.
92. Pikaard, C.S., 2001. Genomic change and gene silencing in polyploids. Trends Genet. 17, 675-677.
93. Prince, V.E., Picket, F.B., 2002. Splitting pairs: the diverging fates of duplicated genes. Nat. Rev. Genet. 3, 827-837.
94. Purugganan, M.D., Rounsley, S.D., Schmidt, R.J., Yanofsky, M.F., 1995. Molecular evolution of flower development: diversification of the plants MADS-box regulatory gene family. Genetics 140, 345-356.
95. Purugganan, M.D., 1997. The MADS-box floral homeotic gene lineages predate the origin of seed plants: phylogenetic and molecular clock estimates. J. Mol. Evol. 45, 392-396.
96. Rask, R., Andreasson, E., Ekbom, B., Eriksson, S., Pontoppidan, B., Meijer, J., 2000. Myrosinase: gene family evolution and herbivore defense in Brassicaceae. Plant Mol. Biol. 42, 93-114.
97. Reinisch, A.J., Dong, J., Brubaker, C.L., Stelly, D.M., Wendel, J.F., Paterson, A.H., 1994. A detailed RFLP map of cotton, Gossypium hirsutum x G. barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138, 829-847.
98. Reiser, L., Sanchez-Baracaldo, P., Hake, S., 2000. Knots in the family tree: evolutionary relationships and functions of knox homeobox genes. Plant Mol. Biol. 42, 151-166.
99. Rieseberg, L.H., 2001. Polyploid evolution: keeping peace at genomic reunions. Curr. Biol. 11, R925-R928.
100. Robichaux, R.H., Carr, G.D., Liebman, M., Pearcy, R.W., 1990. Adaptive radiation of the Hawaiian silversword alliance (Compositae-Madiinae): ecological, morphological and physiological diversity. Ann. Miss. Bot. Gar. 77, 64-72.
101. Rodriguez, D.J., 1996. A model for the establishment of polyploidy in plants. Am. Nat. 147, 33-46.
102. Schmidt, R., 2002. Plant genome evolution: lessons from comparative genomics at the DNA level. Plant Mol. Biol. 48, 21-37.
103. Schranz, M.E., Osborn, T., 2000. Novel flowering time variation in the resynthesized polyploid Brassica napus. J. Heredity 91, 242-246.
104. Schranz, M.E., Quijada, P., Sung, S.-B., Lukens, L., Amasino, R., Osborn, T.C., 2002. Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 162, 1457-1468.
105. Segraves, K., Thompson, J., 1999. Plant polyploidy and pollination: floral traits and insect visits to diploid and tetraploid Heuchera grossulariifolia. Evolution 53, 1114-1127.
106. Segraves, K., Thompson, J.N., Soltis, P.S., Soltis, D.E., 1999. Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia. Mol. Ecol. 8, 253-262.
107. Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y., Shinizaki, K., 2001. Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13, 61-72.
108. Senchina, D.S., Alvarez, I., Cronn, R.C., Biu, B., Rong, J., Noyes, R.D., Paterson, A.H., Wing, R.A., Wilkins, T.A., Wendel, J.F., 2003. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol. Biol. Evol. 20, 633-643.
109. Shaked, H., Kashkush, K., Ozkan, H., Feldman, M., Levy, A.A., 2001. 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.
110. Shoemaker, R.C., Polzin, K., Labate, J., Specht, J., Brummer, E.C., Olson, T., Young, N., Concibido, V., Wilcox, J., Tamulonis, J.P., Kochert, G., Boerma, H.R., 1996. Genome duplication in soybean (Glycine subgenus soja). Genetics 144, 329-338.
111. Sidow, A., 1996. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6, 715-722.
112. Small, R.L., Ryburn, J.A., Wendel, J.F., 1999. Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.). Mol. Biol. Evol. 16, 491-501.
113. Small, R.L., Wendel, J.F., 2000. Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium). Genetics 155, 1913-1926.
114. Small, R.L., Wendel, J.F., 2002. Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Mol. Biol. Evol. 19, 597-607.
115. Soltis, P.S., Soltis, D.E., 1991. Multiple origins of the allotetraploid Tragopogon mirus (Compositae): rDNA evidence. Syst. Bot. 16, 407-413.
116. Soltis, D.E., Soltis, P.S., 1993. Molecular data and the dynamic nature of polyploidy. Crit. Rev. Plant Sci. 12, 243-273.
117. Soltis, D.E., Soltis, P., 1995. The dynamic nature of polyploid genomes. Proc. Natl. Acad. Sci. USA 92, 8089-8091.
118. Soltis, P.S., Plunkett, G.M., Novak, S.J., Soltis, D.E., 1995. Genetic variation in Tragopogon species: additional origins of the allotetraploids T. mirus and T. miscellus (Compositae). Am. J. Bot. 82, 1329-1341.
119. Soltis, D.E., Soltis, P.S., 1999. Polyploidy: recurrent formation and genome evolution. Trends Ecol. Evol. 14, 348-352.
120. Song, K., Lu, P., Osborn, T., 1995. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. USA 92, 8089-8091.
121. Sossey-Alaouni, K., Serieys, H., Tersac, M., Lambert, P., Schilling, E., Griveau, Y., Kaan, F., Berville, A., 1998. Evidence for several genomes in Helianthus. Theor. Appl. Genet. 97, 422-430.
122. Stebbins, G.L., 1950. Variation and Evolution in Plants. Columbia University Press, New York.
123. Stebbings, G.L., 1971. Chromosomal Evolution in Higher Plants. Edward Arnold, London.
124. Sybenga, J., 1996. Chromosome pairing affinity and quadrivalent formation in polyploids: do segmental allopolyploids exist? Genome 39, 1176-1184.
125. The Arabidopsis Genome Initiative, 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
126. Theissen, G., Becker, A., Di Rosa, A., Kanno, A., Kim, J.T., Munster, T., Winter, K.-U., Saedler, H., 2000. A short history of MADS-box genes in plants. Plant Mol. Biol. 42, 115-149.
127. Theissen, G., 2002. Secret life of genes. Nature 415, 741.
128. Thompson, J.D., Lumaret, R., 1992. The evolutionary dynamics of polyploid plants-origins, establishment and persistence. Trends Ecol. Evol. 7, 302-307.
129. Uhl, C.H., 1978. Chromosomes of Mexican Sedum, II Section Pachysedum. Rhodora 80, 491-512.
130. Vandepoele, K., Simillion, C., de Peer, Y., 2002. Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. Trends Genet. 18, 606-608.
131. Vincentz, M., Bandeira-Kobarg, C., Gauer, L., Schloegl, P., Leite, A., 2003. Evolutionary pattern of angiosperm bZIP factors homologous to the maize Opaque2 regulatory protein. J. Mol. Evol. 56, 105-116.
132. Vision, T., Brown, D., Tanksley, S., 2000. The origins of genomic duplications in Arabidopsis. Science 290, 2114-2117.
133. Walsh, J., 1995. How often do duplicated genes evolve new functions? Genetics 139, 421-428.
134. Wendel, J.F., Schnabel, A., Seelanan, T., 1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA 92, 280-284.
135. Wendel, J.F., 2000. Genome evolution in polyploids. Plant Mol. Biol. 42, 225-249.
136. Wendel, J.F., Cronn, R.C., Johnston, J.S., Price, H.J., 2002. Feast and famine in plant genomes. Genetica 115, 37-47.
137. Wilson, H.D., Barber, S.C., Walters, T., 1983. Loss of duplicate gene expression in tetraploid Chenopodium. Biochem. Syst. Ecol. 11, 7-13.
138. Yuan, Q., Hill, J., Hsiao, J., Moffat, K., Ouyang, S., Cheng, Z., Jiang, J., Buell, C.R., 2002. Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol. Gen. Genom. 267, 713-720.
139. Zhang, L.Q., Pond, S.K., Gaut, B.S., 2001. A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa. J. Mol. Evol. 52, 144-156.