Polyploidy and the proteome

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1864, Issue 8, 2016, Pages 896-907

  Soltis, Douglas E ^a,b   Misra, Biswapriya B ^b   Shan, Shengchen ^a,b   Chen, Sixue ^b   Soltis, Pamela S ^a,b  

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

Author keywords

Genome; Polyploidy; Proteome features; Proteomics; Transcriptome; Whole genome duplication

Indexed keywords

PROTEOME; TRANSCRIPTOME; PLANT PROTEIN;

ALLOPOLYPLOIDY; ARTICLE; DUPLICATE GENE; GENE DOSAGE; GENE DUPLICATION; GENE LOSS; GENE SILENCING; GENOMICS; GENOTYPE PHENOTYPE CORRELATION; NONHUMAN; PLANT GENOME; POLYPLOIDY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEOMICS; TRANSCRIPTOMICS; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; PLANT; PROCEDURES;

GENE EXPRESSION PROFILING; PLANT PROTEINS; PLANTS; POLYPLOIDY; PROTEOME; PROTEOMICS;

EID: 84976292739     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2016.03.010     Document Type: Article

References (165)

1. [1] Soltis, D.E., Albert, V.A., Leebens-Mack, J., Bell, C.D., Paterson, A.H., Zheng, C., Sankoff, D., DePamphilis, C.W., Wall, P.K., Soltis, P.S., Polyploidy and angiosperm diversification. Am. J. Bot. 96 (2009), 336–348.
2. [2] Van de Peer, Y., Maere, S., Meyer, A., The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10 (2009), 725–732.
3. [3] Van de Peer, Y., Maere, S., Meyer, A., 2R or not 2R is not the question anymore. Nat. Rev. Genet., 11, 2010, 166.
4. [4] Husband, B.C., Baldwin, S.J., Suda, J., The incidence of polyploidy in natural plant populations: major patterns and evolutionary processes. Greilhuber, J., Dolezel, J., Wendel, J.F., (eds.) Plant Genome Diversity Volume 2, 2013, Springer, Vienna, 255–276.
5. [5] Cañestro, C., Two rounds of whole-genome duplication: evidence and impact on the evolution of vertebrate innovations. Soltis, P.S., Soltis, D.E., (eds.) Polyploidy and Genome Evolution, 2012, Springer, New York, 309–339.
6. [6] Braasch, I., Postlethwait, J., Polyploidy in fish and the teleost genome duplication. Soltis, P.S., Soltis, D.E., (eds.) Polyploidy and Genome Evolution, 2012, Springer, New York, 341–383.
7. [7] Hudson, C., Conant, G., Yeast as a window into changes in genome complexity due to polyploidization. Soltis, P.S., Soltis, D.E., (eds.) Polyploidy and Genome Evolution, 2012, Springer, New York, 293–308.
8. [8] Wood, T.E., Takebayashi, N., Barker, M.S., Mayrose, I., Greenspoon, P.B., Rieseberg, L.H., The frequency of polyploid speciation in vascular plants. Proc. Natl. Acad. Sci. 106 (2009), 13875–13879.
9. [9] Barker, M.S., Wolf, P.G., Unfurling fern biology in the genomics age. Bioscience 60 (2010), 177–185.
10. [10] Jiao, Y., Wickett, N.J., Ayyampalayam, S., Chanderbali, A.S., Landherr, L., Ralph, P.E., Tomsho, L.P., Hu, Y., Liang, H., Soltis, P.S., Soltis, D.E., Clifton, S.W., Schlarbaum, S.E., Schuster, S.C., Ma, H., Leebens-Mack, J., dePamphilis, C.W., Ancestral polyploidy in seed plants and angiosperms. Nature 473 (2011), 97–100.
11. [11] Amborella Genome Project, The Amborella genome and the evolution of flowering plants. Science, 342, 2013, 1241089.
12. [12] Cui, L., Wall, P.K., Leebens-Mack, J.H., Lindsay, B.G., Soltis, D.E., Doyle, J.J., Soltis, P.S., Carlson, J.E., Arumuganathan, K., Barakat, A., Albert, V.A., Ma, H., DePamphilis, C.W., Widespread genome duplications throughout the history of flowering plants. Genome Res. 16 (2006), 738–749.
13. [13] Vanneste, K., Maere, S., Van de Peer, Y., Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philos. Philos. Trans. R. Soc. London B Biol. Sci., 369, 2014, 20130353.
14. [14] Barker, M., Baute, G., Liu, S.L., Duplications and turnover in plant genomes. Wendel, J.F., Greilhuber, J., Dolezel, J., Leitch, I.J., (eds.) Plant Genome Diversity Volume 1, 2012, Springer, Vienna, 155–169.
15. [15] Estep, M.C., McKain, M.R., Vela Diaz, D., Zhong, J., Hodge, J.G., Hodkinson, T.R., Layton, D.J., Malcomber, S.T., Pasquet, R., Kellogg, E. a, Allopolyploidy, diversification, and the Miocene grassland expansion. Proc. Natl. Acad. Sci. 111 (2014), 15149–15154.
16. [16] Tank, D.C., Eastman, J.M., Pennell, M.W., Soltis, P.S., Soltis, D.E., Hinchliff, C.E., Brown, J.W., Sessa, E.B., Harmon, L.J., Nested radiations and the pulse of angiosperm diversification : increased diversification rates often follow whole genome duplications. New Phytol. 207 (2015), 454–467.
17. [17] P.S. Solis, D.E. Soltis, Ancient WGD events as drivers of key innovations in angiosperms. Curr. Opin. Genet. Dev. (in press).
18. [18] Ainouche, M., Chelaifa, H., Ferreira, J., Bellot, S., Ainouche, A., Salmon, A., Polyploid evolution in Spartina: dealing with highly redundant hybrid genomes. Soltis, P.S., Soltis, D.E., (eds.) Polyploidy and Genome Evolution, 2012, Springer, New York, 225–243.
19. [19] Soltis, P.S., Soltis, D.E., The role of genetic and genomic attributes in the success of polyploids. Proc. Natl. Acad. Sci. 97 (2000), 7051–7057.
20. [20] Soltis, P.S., Soltis, D.E., The role of hybridization in plant speciation. Annu. Rev. Plant Biol. 60 (2009), 561–588.
21. [21] Gaeta, R.T., Pires, J.C., Iniguez-Luy, F., Leon, E., Osborn, T.C., Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19 (2007), 3403–3417.
22. [22] Buggs, R.J.A., Zhang, L., Miles, N., Tate, J. a, Gao, L., Wei, W., Schnable, P.S., Barbazuk, W.B., Soltis, P.S., Soltis, D.E., Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant. Curr. Biol. 21 (2011), 551–556.
23. [23] Buggs, R.J.A., Wendel, J.F., Doyle, J.J., Soltis, D.E., Soltis, P.S., Coate, J.E., The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 369, 2014, 20130354.
24. [24] Hegarty, M.J., Abbott, R.J., Hiscock, S.J., Allopolyploid speciation in action: the origins and evolution of Senecio cambrensis. Soltis, P.S., Soltis, D.E., (eds.) Polyploidy and Genome Evolution, 2012, Springer, New York, 245–270.
25. [25] Soltis, D.E., Buggs, R.J.A., Barbazuk, W.B., Chamala, S., Chester, M., Gallagher, J.P., Schnable, P.S., Soltis, P.S., The early stages of polyploidy: rapid and repeated evolution in Tragopogon. Soltis, P.S., Soltis, D.E., (eds.) Polyploidy and Genome Evolution, 2012, Springer, New York, 271–292.
26. [26] Soltis, D.E., Visger, C.J., Soltis, P.S., The polyploidy revolution then…and now: Stebbins revisited. Am. J. Bot. 101 (2014), 1057–1078.
27. [27] Kihara, H., Ono, T., Chromosomenzahlen und systematische Gruppierung der Rumex-Arten. Z. Zellf. Mikroskop. Anat. 4 (1926), 475–481.
28. [28] Müntzing, A., The evolutionary significance of autopolyploidy. Hereditas 21 (1936), 363–378.
29. [29] Darlington, C.D., Recent Advances in Cytology. second ed., 1937, P. Blackiston's, Philadephia.
30. [30] Clausen, J., Keck, D.D., Hiesey, W.M., Experimental studies on the nature of species. II. Plant evolution through amphiploidy, with examples from the Madiinae, 1945, Carnegie Institute of Washington, Washington DC.
31. [31] Stebbins, C.L. Jr., Variation and Evolution in Plants, Oxford Univ. 1950, Press, New York.
32. [32] Grant, V., Plant Speciation. second ed., 1981, Columbia Univ. Press, New York.
33. [33] Lewis, W., Polyploidy in angiosperms: dicotyledons. Lewis, W., (eds.) Polyploidy, 1980, Plenum Press, New York, 241–268.
34. [34] Ohno, S., Evolution by Gene Duplication. 1970, Springer, New York.
35. [35] Lynch, M., Conery, J.S., The evolutionary fate and consequences of duplicate genes. Science 290 (2000), 1151–1155.
36. [36] Doyle, J.J., Flagel, L.E., Paterson, A.H., Rapp, R.A., Soltis, D.E., Soltis, P.S., Wendel, J.F., Evolutionary genetics of genome merger and doubling in plants. Annu. Rev. Genet. 42 (2008), 443–461.
37. [37] Jackson, S., Chen, Z.J., Genomic and expression plasticity of polyploidy. Curr. Opin. Plant Biol. 13 (2010), 153–159.
38. [38] Wang, Y., Wang, X., Paterson, A.H., Genome and gene duplications and gene expression divergence: a view from plants. Ann. N. Y. Acad. Sci. 1256 (2012), 1–14.
39. [39] Yoo, M.J., Liu, X., Pires, J.C., Soltis, P.S., Soltis, D.E., Nonadditive gene expression in polyploids. Annu. Rev. Genet. 48 (2014), 485–517.
40. [40] Paterson, A.H., Chapman, B.A., Kissinger, J.C., Bowers, J.E., Feltus, F.A., Estill, J.C., Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet. 22 (2006), 597–602.
41. [41] De Smet, R., Adams, K.L., Vandepoele, K., Van Montagu, M.C.E., Maere, S., Van de Peer, Y., Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc. Natl. Acad. Sci. 110 (2013), 2898–2903.
42. [42] Chapman, B.A., Bowers, J.E., Feltus, F. a, Paterson, A.H., Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc. Natl. Acad. Sci. 103 (2006), 2730–2735.
43. [43] Barker, M.S., Kane, N.C., Matvienko, M., Kozik, A., Michelmore, R.W., Knapp, S.J., Rieseberg, L.H., Multiple paleopolyploidizations during the evolution of the compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol. 25 (2008), 2445–2455.
44. [44] Buggs, R.J.A., Chamala, S., Wu, W., Tate, J.A., Schnable, P.S., Soltis, D.E., Soltis, P.S., Barbazuk, W.B., Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Curr. Biol. 22 (2012), 248–252.
45. [45] Chaudhary, B., Flagel, L., Stupar, R.M., Udall, J.A., Verma, N., Springer, N.M., Wendel, J.F., Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium). Genetics 182 (2009), 503–517.
46. [46] Wendel, J., Flagel, L., Adams, K., Jeans, Genes, and Genomes: Cotton as a Model for Studying Polyploidy. Soltis, P.S., Soltis, D.E., (eds.) Polyploidy and Genome Evolution, 2012, Springer, New York, 181–207.
47. [47] Bowers, J.E., Chapman, B.A., Rong, J., Paterson, A.H., Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422 (2003), 433–438.
48. [48] Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., Bai, Y., Mun, J.-H., Bancroft, I., Cheng, F., Huang, S., Li, X., Hua, W., Wang, J., Wang, X., Freeling, M., Pires, J.C., Paterson, A.H., Chalhoub, B., Wang, B., et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43 (2011), 1035–1039.
49. [49] Gaut, B.S., Doebley, J.F., DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. 94 (1997), 6809–6814.
50. [50] Paterson, A.H., Wang, Z., Li, J., Tang, H., Ancient and recent polyploidy in the monocots. Soltis, P.S., Soltis, D.E., (eds.) Polyploidy and Genome Evolution, 2012, Springer, New York, 93–108.
51. [51] Thomas, B.C., Pedersen, B., Freeling, M., Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 16 (2006), 934–946.
52. [52] Schnable, J.C., Springer, N.M., Freeling, M., Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. 108 (2011), 4069–4074.
53. [53] Freeling, M., Woodhouse, M.R., Subramaniam, S., Turco, G., Lisch, D., Schnable, J.C., Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr. Opin. Plant Biol. 15 (2012), 131–139.
54. [54] Schnable, J.C., Freeling, M., Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLoS One, 6, 2011, e17855.
55. [55] Birchler, J.A., Veitia, R.A., The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19 (2007), 395–402.
56. [56] Birchler, J.A., Veitia, R.A., Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc. Natl. Acad. Sci. 109 (2012), 14746–14753.
57. [57] Freeling, M., Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60 (2009), 433–453.
58. [58] Maere, S., De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., Van de Peer, Y., Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. 102 (2005), 5454–5459.
59. [59] Hahn, M.W., Distinguishing among evolutionary models for the maintenance of gene duplicates. J. Hered. 100 (2009), 605–617.
60. [60] Bekaert, M., Edger, P.P., Pires, J.C., Conant, G.C., Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Plant Cell 23 (2011), 1719–1728.
61. [61] Tang, H., Woodhouse, M.R., Cheng, F., Schnable, J.C., Pedersen, B.S., Conant, G., Wang, X., Freeling, M., Pires, J.C., Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 190 (2012), 1563–1574.
62. [62] Buggs, R.J.A., Elliott, N.M., Zhang, L., Koh, J., Viccini, L.F., Soltis, D.E., Soltis, P.S., Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus. New Phytol. 186 (2010), 175–183.
63. [63] Taylor, J.S., Raes, J., Duplication and divergence: the evolution of new genes and old ideas. Annu. Rev. Genet. 38 (2004), 615–643.
64. [64] Comai, L., Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12 (2000), 1551–1568.
65. [65] Wendel, J.F., Genome evolution in polyploids. Plant Mol. Biol. 42 (2000), 225–249.
66. [66] Prince, V.E., Pickett, F.B., Splitting pairs: the diverging fates of duplicated genes. Nat. Rev. Genet. 3 (2002), 827–837.
67. [67] Chagué, V., Just, J., Mestiri, I., Balzergue, S., Tanguy, A.M., Huneau, C., Huteau, V., Belcram, H., Coriton, O., Jahier, J., Chalhoub, B., Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids. New Phytol. 187 (2010), 1181–1194.
68. [68] Tate, J.A., Soltis, D.E., Soltis, P.S., Polyploidy in plants. Gregory, T.R., (eds.) The Evolution of the Genome, 2005, Elsevier, San Diego, California, 371–426.
69. [69] Xiong, Z., Gaeta, R.T., Pires, J.C., Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc. Natl. Acad. Sci. 108 (2011), 7908–7913.
70. [70] Chester, M., Gallagher, J.P., Symonds, V.V., Cruz da Silva, A.V., Mavrodiev, E.V., Leitch, A.R., Soltis, P.S., Soltis, D.E., Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc. Natl. Acad. Sci. 109 (2012), 1176–1181.
71. [71] Feldman, M., Liu, B., Segal, G., Abbo, S., Levy, A.A., Vega, J.M., Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics 147 (1997), 1381–1387.
72. [72] Ozkan, H., Levy, A.A., Feldman, M., Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops–Triticum) group. Plant Cell 13 (2001), 1735–1747.
73. [73] Shaked, H., Kashkush, K., Ozkan, H., Feldman, M., Levy, A.A., Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13 (2001), 1749–1759.
74. [74] Kashkush, K., Feldman, M., Levy, A.A., Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160 (2002), 1651–1659.
75. [75] Buggs, R.J.A., Doust, A.N., Tate, J.A., Koh, J., Soltis, K., Feltus, F.A., Paterson, A.H., Soltis, P.S., Soltis, D.E., Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity 103 (2009), 73–81.
76. [76] Feng, S., Jacobsen, S.E., Reik, W., Epigenetic reprogramming in plant and animal development. Science 330 (2010), 622–627.
77. [77] Bender, J., DNA methylation and epigenetics. Annu. Rev. Plant Biol. 55 (2004), 41–68.
78. [78] Coate, J.E., Doyle, J.J., Quantifying whole transcriptome size, a prerequisite for understanding transcriptome evolution across species: an example from a plant allopolyploid. Genome Biol. Evol. 2 (2010), 534–546.
79. [79] Flagel, L.E., Wendel, J.F., Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytol. 186 (2010), 184–193.
80. [80] Lee, H.S., Chen, Z.J., Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. 98 (2001), 6753–6758.
81. [81] Wang, J., Tian, L., Madlung, A., Lee, H.S., Chen, M., Lee, J.J., Watson, B., Kagochi, T., Comai, L., Chen, Z.J., Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167 (2004), 1961–1973.
82. [82] Scheid, O.M., Afsar, K., Paszkowski, J., Formation of stable epialleles and their paramutation-like interaction in tetraploid Arabidopsis thaliana. Nat. Genet. 34 (2003), 450–454.
83. [83] Pikaard, C.S., Chen, Z.J., Nucleolar Dominance. Paule, M.R., (eds.) RNA Polymerase I: Transcription of Eukaryotic Ribosomal RNA, 1998, R.G. Landes, Austin, 275–293.
84. [84] Pikaard, C.S., Nucleolar dominance and silencing of transcription. Trends Plant Sci. 4 (1999), 478–483.
85. [85] Pikaard, C.S., Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids. Plant Mol. Biol. 43 (2000), 163–177.
86. [86] Chen, Z.J., Comai, L., Pikaard, C.S., Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc. Natl. Acad. Sci. 95 (1998), 14891–14896.
87. [87] Chen, Z.J., Pikaard, C.S., Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica. Proc. Natl. Acad. Sci. 94 (1997), 3442–3447.
88. [88] Lynch, M., Force, A., The probability of duplicate gene preservation by subfunctionalization. Genetics 154 (2000), 459–473.
89. [89] Adams, K.L., Cronn, R., Percifield, R., Wendel, J.F., Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. 100 (2003), 4649–4654.
90. [90] Ganko, E.W., Meyers, B.C., Vision, T.J., Divergence in expression between duplicated genes in Arabidopsis. Mol. Biol. Evol. 24 (2007), 2298–2309.
91. [91] Rutter, M.T., Cross, K.V., Van Woert, P.A., Birth, death and subfunctionalization in the Arabidopsis genome. Trends Plant Sci. 17 (2012), 204–212.
92. [92] Roulin, A., Auer, P.L., Libault, M., Schlueter, J., Farmer, A., May, G., Stacey, G., Doerge, R.W., Jackson, S.A., The fate of duplicated genes in a polyploid plant genome. Plant J. 73 (2013), 143–153.
93. [93] Leitch, I.J., Bennett, M.D., Genome downsizing in polyploid plants. Biol. J. Linn. Soc. 82 (2004), 651–663.
94. [94] 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., Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19 (2003), 141–147.
95. [95] Senerchia, N., Felber, F., Parisod, C., Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 282, 2015, 20142874.
96. [96] Chen, S., Harmon, A.C., Advances in plant proteomics. Proteomics 6 (2006), 5504–5516.
97. [97] Albertin, W., Brabant, P., Catrice, O., Eber, F., Jenczewski, E., Chèvre, A.M., Thiellement, H., Autopolyploidy in cabbage (Brassica oleracea L) does not alter significantly the proteomes of green tissues. Proteomics 5 (2005), 2131–2139.
98. [98] Albertin, W., Balliau, T., Brabant, P., Chèvre, A.M., Eber, F., Malosse, C., Thiellement, H., Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics 173 (2006), 1101–1113.
99. [99] Albertin, W., Alix, K., Balliau, T., Brabant, P., Davanture, M., Malosse, C., Valot, B., Thiellement, H., Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization. BMC Genomics 8 (2007), 56–70.
100. [100] Carpentier, S.C., Panis, B., Renaut, J., Samyn, B., Vertommen, A., Vanhove, A.C., Swennen, R., Sergeant, K., The use of 2D-electrophoresis and de novo sequencing to characterize inter- and intra-cultivar protein polymorphisms in an allopolyploid crop. Phytochemistry 72 (2011), 1243–1250.
101. [101] Jacoby, R.P., Millar, A.H., Taylor, N.L., Investigating the role of respiration in plant salinity tolerance by analyzing mitochondrial proteomes from wheat and a salinity-tolerant amphiploid (wheat × Lophopyrum elongatum). J. Proteome Res. 12 (2013), 4807–4829.
102. [102] Kosová, K., Vítámvás, P., Planchon, S., Renaut, J., Vanková, R., Prášil, I.T., Proteome analysis of cold response in spring and winter wheat (Triticum aestivum) crowns reveals similarities in stress adaptation and differences in regulatory processes between the growth habits. J. Proteome Res. 12 (2013), 4830–4845.
103. [103] Koh, J., Chen, S., Zhu, N., Yu, F., Soltis, P.S., Soltis, D.E., Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents. New Phytol. 196 (2012), 292–305.
104. [104] Hu, G., Koh, J., Yoo, M.J., Grupp, K., Chen, S., Wendel, J.F., Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense. New Phytol. 200 (2013), 570–582.
105. [105] Hu, G., Koh, J., Yoo, M.J., Pathak, D., Chen, S., Wendel, J., Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.). Planta 240 (2014), 1237–1251.
106. [106] Hu, G., Koh, J., Yoo, M.J., Chen, S., Wendel, J.F., Gene-expression novelty in allopolyploid cotton: a proteomic perspective. Genetics 200 (2015), 91–104.
107. [107] Shen, Y., Zhang, Y., Zou, J., Meng, J., Wang, J., Comparative proteomic study on Brassica hexaploid and its parents provides new insights into the effects of polyploidization. J. Proteome 112 (2015), 274–284.
108. [108] Alvarez, S., Roy Choudhury, S., Sivagnanam, K., Hicks, L.M., Pandey, S., Quantitative proteomics analysis of Camelina sativa seeds overexpressing the AGG3 gene to identify the proteomic basis of increased yield and stress tolerance. J. Proteome Res. 14 (2015), 2606–2616.
109. [109] Hu, J., Rampitsch, C., Bykova, N.V., Advances in plant proteomics toward improvement of crop productivity and stress resistance. Front. Plant Sci. 6 (2015), 1–15.
110. [110] Wang, J., Tian, L., Lee, H.S., Wei, N.E., Jiang, H., Watson, B., Madlung, A., Osborn, T.C., Doerge, R.W., Comai, L., Chen, Z.J., Genomewide nonadditive gene regulation in Arabidopsis Allotetraploids. Genetics 172 (2006), 507–517.
111. [111] Hu, G., Houston, N.L., Pathak, D., Schmidt, L., Thelen, J.J., Wendel, J.F., Genomically biased accumulation of seed storage proteins in allopolyploid cotton. Genetics 189 (2011), 1103–1115.
112. [112] Yaakov, B., Kashkush, K., Methylation, transcription, and rearrangements of transposable elements in synthetic allopolyploids. Int. J. Plant Genomics, 2011, 2011, 569826.
113. [113] Song, K., Lu, P., Tang, K., Osborn, T.C., Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. 92 (1995), 7719–7723.
114. [114] Adams, K.L., Percifield, R., Wendel, J.F., Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168 (2004), 2217–2226.
115. [115] Skalická, K., Lim, K.Y., Matyasek, R., Matzke, M., Leitch, A.R., Kovarik, A., Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco. New Phytol. 166 (2005), 291–303.
116. [116] Wang, J., Tian, L., Lee, H.S., Wei, N.E., Jiang, H., Watson, B., Madlung, A., Osborn, T.C., Doerge, R.W., Comai, L., Chen, Z.J., Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172 (2006), 507–517.
117. [117] Bahrman, N., Thiellement, H., Parental genome expression in synthetic wheats (Triticum turgidum sp. × T. tauschii sp.) revealed by two-dimensional electrophoresis of seedling proteins. Theor. Appl. Genet. 74 (1987), 218–223.
118. [118] Islam, N., Tsujimoto, H., Hirano, H., Proteome analysis of diploid, tetraploid and hexaploid wheat: towards understanding genome interaction in protein expression. Proteomics 3 (2003), 549–557.
119. [119] Ng, D.W.K., Zhang, C., Miller, M., Shen, Z., Briggs, S.P., Chen, Z.J., Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity 108 (2012), 419–430.
120. [120] McClintock, B., The significance of responses of the genome to challenge. Science 226 (1984), 792–801.
121. [121] Hegarty, M.J., Barker, G.L., Wilson, I.D., Abbott, R.J., Edwards, K.J., Hiscock, S.J., Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Curr. Biol. 16 (2006), 1652–1659.
122. [122] Gaeta, R.T., Pires, J.C., Iniguez-Luy, F., Leon, E., Osborn, T.C., Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19 (2007), 3403–3417.
123. [123] Marmagne, A., Brabant, P., Thiellement, H., Alix, K., Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation. New Phytol. 186 (2010), 216–227.
124. [124] Koh, J., Chen, G., Yoo, M.J., Zhu, N., Dufresne, D., Erickson, J.E., Shao, H., Chen, S., Comparative proteomic analysis of Brassica napus in response to drought stress. J. Proteome Res. 14 (2015), 3068–3081.
125. [125] Jia, H., Shao, M., He, Y., Guan, R., Chu, P., Jiang, H., Proteome dynamics and physiological responses to short-term salt stress in Brassica napus leaves. PLoS One, 10, 2015, e0144808.
126. [126] Kong, F., Mao, S., Jiang, J., Wang, J., Fang, X., Wang, Y., Proteomic changes in newly synthesized Brassica napus allotetraploids and their early generations. Plant Mol. Biol. Report. 29 (2011), 927–935.
127. [127] Wang, X.C., Li, Q., Jin, X., Xiao, G.H., Liu, G.J., Liu, N.J., Qin, Y.M., Quantitative proteomics and transcriptomics reveal key metabolic processes associated with cotton fiber initiation. J. Proteome 114 (2015), 16–27.
128. [128] Gancel, A.L., Grimplet, J., Sauvage, F.X., Ollitrault, P., Brillouet, E.M., Predominant expression of diploid mandarin leaf proteome in two citrus mandarin-derived somatic allotetraploid hybrids. J. Agric. Food Chem. 54 (2006), 6212–6218.
129. [129] Carpentier, S., Exploring the potential of genetic diversity via proteomics: past, present, and future perspectives for banana. Ahuja, R.M., Jain, M.S., (eds.) Genetic Diversity and Erosion in Plants: Indicators and Prevention, 2015, Springer International Publishing, Switzerland, 311–323.
130. [130] Vanhove, A.C., Vermaelen, W., Swennen, R., Carpentier, S.C., A look behind the screens: characterization of the HSP70 family during osmotic stress in a non-model crop. J. Proteome 119 (2015), 10–20.
131. [131] Bancel, E., Bonnot, T., Davanture, M., Branlard, G., Zivy, M., Martre, P., Proteomic approach to identify nuclear proteins in wheat grain. J. Proteome Res. 14 (2015), 4432–4439.
132. [132] Havanapan, P.O., Bourchookarn, A., Ketterman, A.J., Krittanai, C., Comparative proteome analysis of rubber latex serum from pathogenic fungi tolerant and susceptible rubber tree (Hevea brasiliensis). J. Proteome 131 (2016), 82–92.
133. [133] Dai, L., Kang, G., Nie, Z., Li, Y., Zeng, R., Comparative proteomic analysis of latex from Hevea brasiliensis treated with ethyl and methyl jasmonate using iTRAQ-coupled two-dimensional LC–MS/MS. J. Proteome 132 (2016), 167–175.
134. [134] Rahman, A.Y.A., Usharraj, A.O., Misra, B.B., Thottathil, G.P., Jayasekaran, K., Feng, Y., Hou, S., Ong, S.Y., Ng, F.L., Lee, L.S., Tan, H.S., Sakaff, M.K.L.M., Teh, B.S., Khoo, B.F., Badai, S.S., Aziz, N.A., Yuryev, A., Knudsen, B., Dionne-Laporte, A., Mchunu, N.P., et al. Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics 14 (2013), 1–15.
135. [135] Wong, P.F., Abubakar, S., Post-germination changes in Hevea brasiliensis seeds proteome. Plant Sci. 169 (2005), 303–311.
136. [136] Dai, L., Kang, G., Li, Y., Nie, Z., Duan, C., Zeng, R., In-depth proteome analysis of the rubber particle of Hevea brasiliensis (para rubber tree). Plant Mol. Biol. 82 (2013), 155–168.
137. [137] Xiang, Q., Xia, K., Dai, L., Kang, G., Li, Y., Nie, Z., Duan, C., Zeng, R., Proteome analysis of the large and the small rubber particles of Hevea brasiliensis using 2D-DIGE. Plant Physiol. Biochem. 60 (2012), 207–213.
138. [138] Wang, X., Shi, M., Lu, X., Ma, R., Wu, C., Guo, A., Peng, M., Tian, W., A method for protein extraction from different subcellular fractions of laticifer latex in Hevea brasiliensis compatible with 2-DE and MS. Proteome Sci. 8 (2010), 1–10.
139. [139] An, F., Fan, J., Li, J., Li, Q.X., Li, K., Zhu, W., Wen, F., Carvalho, L.J.C.B., Chen, S., Comparison of leaf proteomes of cassava (Manihot esculenta Crantz) cultivar NZ199 diploid and autotetraploid genotypes. PLoS One, 9, 2014, e85991.
140. − accumulation behaviour. J. Plant Physiol. 170 (2013), 1101–1112.
141. [141] Wang, Z., Wang, M., Liu, L., Meng, F., Physiological and proteomic responses of diploid and tetraploid black locust (Robinia pseudoacacia L.) subjected to salt stress. Int. J. Mol. Sci. 14 (2013), 20299–20325.
142. [142] Pacheco, C.M., Pestana-Calsa, M.C., Gozzo, F.C., Mansur Custodio Nogueira, R.J., Menossi, M., Calsa, T., Differentially delayed root proteome responses to salt stress in sugar cane varieties. J. Proteome Res. 12 (2013), 5681–5695.
143. [143] Heringer, A.S., Barroso, T., Macedo, A.F., Santa-Catarina, C., Souza, G.H.M.F., Floh, E.I.S., de Souza-Filho, G.A., Silveira, V., Label-free quantitative proteomics of embryogenic and non-embryogenic callus during sugarcane somatic embryogenesis. PLoS One, 10, 2015, e0127803.
144. [144] Koh, J., Soltis, P.S., Soltis, D.E., Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae). BMC Genomics, 11, 2010, 97.
145. [145] Wang, J., Tian, L., Lee, H.S., Chen, Z.J., Nonadditive regulation of FRI and FLC loci mediates flowering-time variation in Arabidopsis allopolyploids. Genetics 173 (2006), 965–974.
146. [146] Ni, Z., Kim, E.D., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., Chen, Z.J., Altered circadian rhythms regulate growth vigor in hybrids and allopolyploids. Nature 457 (2009), 327–331.
147. [147] Braszewska-Zalewska, A., Dziurlikowska, A., Maluszynska, J., Histone H3 methylation patterns in Brassica nigra, Brassica juncea, and Brassica carinata species. Genome 55 (2011), 68–74.
148. [148] Vogel, C., Marcotte, E.M., Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 13 (2012), 227–232.
149. [149] Anderson, L., Seilhamer, J., A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18 (1997), 533–537.
150. [150] Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H., Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 (1999), 994–999.
151. [151] Maier, T., Güell, M., Serrano, L., Correlation of mRNA and protein in complex biological samples. FEBS Lett. 583 (2009), 3966–3973.
152. [152] Schwanhausser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., Selbach, M., Global quantification of mammalian gene expression control. Nature 473 (2011), 337–342.
153. [153] Hegarty, M., Hiscock, S., Polyploidy: doubling up for evolutionary success. Curr. Biol. 17 (2007), R927–R929.
154. [154] Li, L., Huang, Y., Xia, X., Sun, Z., Preferential duplication in the sparse part of yeast protein interaction network. Mol. Biol. Evol. 23 (2006), 2467–2473.
155. [155] Veitia, R.A., Bottani, S., Birchler, J.A., Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Trends Genet. 24 (2008), 390–397.
156. [156] Stevenson, S.E., Chu, Y., Ozias-Akins, P., Thelen, J.J., Validation of gel-free, label-free quantitative proteomics approaches: applications for seed allergen profiling. J. Proteome 72 (2009), 555–566.
157. [157] Chalhoub, B., Denoeud, F., Liu, S., Parkin, I.A.P., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., Corréa, M., Da Silva, C., Just, J., Falentin, C., Koh, C.S., Le Clainche, I., Bernard, M., Bento, P., Noel, B., Labadie, K., et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345 (2014), 950–953.
158. [158] Coate, J.E., Bar, H., Doyle, J.J., Extensive translational regulation of gene expression in an Allopolyploid (Glycine dolichocarpa). Plant Cell 26 (2014), 136–150.
159. [159] Barbazuk, W.B., Fu, Y., McGinnis, K.M., Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res. 18 (2008), 1381–1392.
160. [160] Syed, N.H., Kalyna, M., Marquez, Y., Barta, A., Brown, J.W.S., Alternative splicing in plants — coming of age. Trends Plant Sci. 17 (2012), 616–623.
161. [161] Reddy, A.S.N., Marquez, Y., Kalyna, M., Barta, A., Complexity of the alternative splicing landscape in plants. Plant Cell 25 (2013), 3657–3683.
162. [162] Marquez, Y., Brown, J.W.S., Simpson, C., Barta, A., Kalyna, M., Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 22 (2012), 1184–1195.
163. [163] Roose, M.L., Gottlieb, L.D., Genetic and biochemical consequences of polyploidy in Tragopogon. Evolution 30 (1976), 818–830.
164. [164] Roose, M.L., Gottlieb, L.D., Biochemical properties and level of expression of alcohol dehydrogenases in the allotetraploid plant Tragopogon miscellus and its diploid progenitors. Biochem. Genet. 18 (1980), 1065–1085.
165. [165] Bianco, L., Lopez, L., Scalone, A.G., Di Carli, M., Desiderio, A., Benvenuto, E., Perrotta, G., Strawberry proteome characterization and its regulation during fruit ripening and in different genotypes. J. Proteome 72 (2009), 586–607.