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Annual Review of Genetics

Volume 48, 2014

Nonadditive Gene Expression in Polyploids

Abstract

Allopolyploidy involves hybridization and duplication of divergent parental genomes and provides new avenues for gene expression. The expression levels of duplicated genes in polyploids can show deviation from parental additivity (the arithmetic average of the parental expression levels). Nonadditive expression has been widely observed in diverse polyploids and comprises at least three possible scenarios: () The total gene expression level in a polyploid is similar to that of one of its parents (expression-level dominance); () total gene expression is lower or higher than in both parents (transgressive expression); and () the relative contribution of the parental copies (homeologs) to the total gene expression is unequal (homeolog expression bias). Several factors may result in expression nonadditivity in polyploids, including maternal-paternal influence, gene dosage balance, - and/or -regulatory networks, and epigenetic regulation. As our understanding of nonadditive gene expression in polyploids remains limited, a new generation of investigators should explore additional phenomena (i.e., alternative splicing) and use other high-throughput “omics” technologies to measure the impact of nonadditive expression on phenotype, proteome, and metabolome.

Keyword(s): additivity, alternative splicing, expression-level dominance, genome duplication, homeolog expression bias, transgressive expression
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2014-11-23
2024-04-26
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Literature Cited

  1. Adams KL, Cronn R, Percifield R, Wendel JF. 1.  2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA 100:4649–54 [Google Scholar]
  2. Adams KL, Percifield R, Wendel JF. 2.  2004. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168:2217–26 [Google Scholar]
  3. Adams KL, Wendel JF. 3.  2004. Exploring the genomic mysteries of polyploidy in cotton. Biol. J. Linn. Soc. 82:573–81 [Google Scholar]
  4. Adams KL, Wendel JF. 4.  2005. Allele-specific, bidirectional silencing of an alcohol dehydrogenase gene in different organs of interspecific diploid cotton hybrids. Genetics 171:2139–42 [Google Scholar]
  5. Adams KL, Wendel JF. 5.  2005. Novel patterns of gene expression in polyploid plants. Trends Genet. 21:539–43 [Google Scholar]
  6. Ainouche M, Chelaifa H, Ferreira J, Bellot S, Ainouche A, Salmon A. 6.  2012. Polyploid evolution in Spartina: dealing with highly redundant hybrid genomes. See Ref. 166 225–44
  7. Akama S, Shimizu-Inatsugi R, Shimizu KK, Sese J. 7.  2014. Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis. Nucleic Acids Res. 42:e46 [Google Scholar]
  8. Akhunova AR, Matniyazov RT, Liang H, Akhunov ED. 8.  2010. Homoeolog-specific transcriptional bias in allopolyploid wheat. BMC Genomics 11:505 [Google Scholar]
  9. Albertin W, Alix K, Balliau T, Brabant P, Davanture M. 9.  et al. 2007. Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization. BMC Genomics 8:56 [Google Scholar]
  10. Albertin W, Balliau T, Brabant P, Chevre AM, Eber F. 10.  et al. 2006. Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics 173:1101–13 [Google Scholar]
  11. Barbazuk WB, Fu Y, McGinnis KM. 11.  2008. Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res. 18:1381–92 [Google Scholar]
  12. Bardil A, de Almeida JD, Combes MC, Lashermes P, Bertrand B. 12.  2011. Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature. New Phytol. 192:760–74 [Google Scholar]
  13. Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW. 13.  et al. 2008. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol. 25:2445–55 [Google Scholar]
  14. Bekaert M, Edger PP, Hudson CM, Pires JC, Conant GC. 14.  2012. Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis. New Phytol. 196:596–605 [Google Scholar]
  15. Bekaert M, Edger PP, Pires JC, Conant GC. 15.  2011. Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Plant Cell 23:1719–28 [Google Scholar]
  16. Birchler JA, Veitia RA. 16.  2012. Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc. Natl. Acad. Sci. USA 109:14746–53 [Google Scholar]
  17. Blanc G, Wolfe KH. 17.  2004. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679–91 [Google Scholar]
  18. Blanc G, Wolfe KH. 18.  2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667–78 [Google Scholar]
  19. Bottley A, Xia GM, Koebner RM. 19.  2006. Homoeologous gene silencing in hexaploid wheat. Plant J. 47:897–906 [Google Scholar]
  20. Buggs RJ, Chamala S, Wu W, Gao L, May GD. 20.  et al. 2010. Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol. Ecol. 19:Suppl. 1132–46 [Google Scholar]
  21. Buggs RJ, Chamala S, Wu W, Tate JA, Schnable PS. 21.  et al. 2012. Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Curr. Biol. 22:248–52 [Google Scholar]
  22. Buggs RJ, Wendel JF, Doyle JJ, Soltis DE, Soltis PS, Coate JE. 22.  2014. The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos. Trans. R. Soc. B 369:pi:20130354 [Google Scholar]
  23. Buggs RJ, Zhang L, Miles N, Tate JA, Gao L. 23.  et al. 2011. Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant. Curr. Biol. 21:551–56 [Google Scholar]
  24. Carpentier SC, Panis B, Renaut J, Samyn B, Vertommen A. 24.  et al. 2011. The use of 2D-electrophoresis and de novo sequencing to characterize inter- and intra-cultivar protein polymorphisms in an allopolyploid crop. Phytochemistry 72:1243–50 [Google Scholar]
  25. Cenci A, Combes MC, Lashermes P. 25.  2012. Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments. Plant Mol. Biol. 78:135–45 [Google Scholar]
  26. Chague V, Just J, Mestiri I, Balzergue S, Tanguy AM. 26.  et al. 2010. Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids. New Phytol. 187:1181–94 [Google Scholar]
  27. Chang PL, Dilkes BP, McMahon M, Comai L, Nuzhdin SV. 27.  2010. Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biol. 11:R125 [Google Scholar]
  28. Chase CD. 28.  2007. Cytoplasmic male sterility: a window to the world of plant mitochondrial-nuclear interactions. Trends Genet. 23:81–90 [Google Scholar]
  29. Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N. 29.  et al. 2009. Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium). Genetics 182:503–17 [Google Scholar]
  30. Chelaifa H, Mahe F, Ainouche M. 30.  2010. Transcriptome divergence between the hexaploid salt-marsh sister species Spartina maritima and Spartina alterniflora (Poaceae). Mol. Ecol. 19:2050–63 [Google Scholar]
  31. Chelaifa H, Monnier A, Ainouche M. 31.  2010. Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina×townsendii and Spartina anglica (Poaceae). New Phytol. 186:161–74 [Google Scholar]
  32. Chen TW, Wu TH, Ng WV, Lin WC. 32.  2011. Interrogation of alternative splicing events in duplicated genes during evolution. BMC Genomics 12:Suppl. 3S16 [Google Scholar]
  33. Chen ZJ. 33.  2007. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu. Rev. Plant Biol. 58:377–406 [Google Scholar]
  34. Chen ZJ. 34.  2010. Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci. 15:57–71 [Google Scholar]
  35. Chen ZJ, Pikaard CS. 35.  1997. Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev. 11:2124–36 [Google Scholar]
  36. Chen ZJ, Pikaard CS. 36.  1997. Transcriptional analysis of nucleolar dominance in polyploid plants: Biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica. Proc. Natl. Acad. Sci. USA 94:3442–47 [Google Scholar]
  37. Cheng F, Wu J, Fang L, Sun S, Liu B. 37.  et al. 2012. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLOS ONE 7:e36442 [Google Scholar]
  38. Chester M, Gallagher JP, Symonds VV, Cruz da Silva AV, Mavrodiev EV. 38.  et al. 2012. Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc. Natl. Acad. Sci. USA 109:1176–81 [Google Scholar]
  39. Clausen J, Keck DD, Hiesey WM. 39.  1945. Experimental Studies on the Nature of Species. II Plant Evolution Through Amphiploidy and Autopolyploidy, with Examples from the Madiinae. Washington, DC: Carnegie Inst. Wash.
  40. Coate JE, Bar H, Doyle JJ. 40.  2014. Extensive translational regulation of gene expression in an allopolyploid (Glycine dolichocarpa). Plant Cell 26:136–50 [Google Scholar]
  41. Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH. 41.  et al. 2000. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12:1551–67 [Google Scholar]
  42. Combes MC, Cenci A, Baraille H, Bertrand B, Lashermes P. 42.  2012. Homeologous gene expression in response to growing temperature in a recent allopolyploid (Coffea arabica L.). J. Hered. 103:36–46 [Google Scholar]
  43. Combes MC, Dereeper A, Severac D, Bertrand B, Lashermes P. 43.  2013. Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures. New Phytol. 200:251–60 [Google Scholar]
  44. Conant GC, Birchler JA, Pires JC. 44.  2014. Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Curr. Opin. Plant Biol. 19:91–98 [Google Scholar]
  45. Conant GC, Wolfe KH. 45.  2008. Turning a hobby into a job: how duplicated genes find new functions. Nat. Rev. Genet. 9:938–50 [Google Scholar]
  46. Darlington CD. 46.  1937. Recent Advances in Cytology Philadelphia, PA: P. Blakiston's Son Co.
  47. Des Marais DL, Rausher MD. 47.  2008. Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454:762–65 [Google Scholar]
  48. Doyle JJ, Doyle JL, Rauscher JT, Brown AHD. 48.  2004. Evolution of the perennial soybean polyploid complex (Glycine subgenus Glycine): a study of contrasts. Biol. J. Linn. Soc. 82:583–97 [Google Scholar]
  49. Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE. 49.  et al. 2008. Evolutionary genetics of genome merger and doubling in plants. Annu. Rev. Genet. 42:443–61 [Google Scholar]
  50. Drechsel G, Kahles A, Kesarwani AK, Stauffer E, Behr J. 50.  et al. 2013. Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome. Plant Cell 25:3726–42 [Google Scholar]
  51. Feldman M, Liu B, Segal G, Abbo S, Levy AA, Vega JM. 51.  1997. Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics 147:1381–87 [Google Scholar]
  52. Flagel L, Udall J, Nettleton D, Wendel J. 52.  2008. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biol. 6:16 [Google Scholar]
  53. Flagel LE, Chen L, Chaudhary B, Wendel JF. 53.  2009. Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton. J. Hered. 100:487–90 [Google Scholar]
  54. Flagel LE, Wendel JF. 54.  2010. Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytol. 186:184–93 [Google Scholar]
  55. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 55.  1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531–45 [Google Scholar]
  56. Freeling M. 56.  2009. Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60:433–53 [Google Scholar]
  57. Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC. 57.  2007. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19:3403–17 [Google Scholar]
  58. Gaeta RT, Yoo SY, Pires JC, Doerge RW, Chen ZJ, Osborn TC. 58.  2009. Analysis of gene expression in resynthesized Brassica napus allopolyploids using Arabidopsis 70mer oligo microarrays. PLOS ONE 4:e4760 [Google Scholar]
  59. Gancel AL, Grimplet J, Sauvage FX, Ollitrault P, Brillouet JM. 59.  2006. Predominant expression of diploid mandarin leaf proteome in two citrus mandarin-derived somatic allotetraploid hybrids. J. Agric. Food Chem. 54:6212–18 [Google Scholar]
  60. Garsmeur O, Schnable JC, Almeida A, Jourda C, D'Hont A, Freeling M. 60.  2014. Two evolutionarily distinct classes of paleopolyploidy. Mol. Biol. Evol. 31:448–54 [Google Scholar]
  61. Gong L, Salmon A, Yoo MJ, Grupp KK, Wang Z. 61.  et al. 2012. The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco. Mol. Biol. Evol. 29:3023–36 [Google Scholar]
  62. Gottlieb LD. 62.  2003. Plant polyploidy: gene expression and genetic redundancy. Heredity 91:91–92 [Google Scholar]
  63. Grant V. 63.  1981. Plant Speciation New York: Columbia Univ. Press
  64. Grover CE, Gallagher JP, Szadkowski EP, Yoo MJ, Flagel LE, Wendel JF. 64.  2012. Homoeolog expression bias and expression level dominance in allopolyploids. New Phytol. 196:966–71 [Google Scholar]
  65. Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF. 65.  2004. Incongruent patterns of local and global genome size evolution in cotton. Genome Res. 14:1474–82 [Google Scholar]
  66. Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF. 66.  2007. Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant J. 50:995–1006 [Google Scholar]
  67. Ha M, Kim ED, Chen ZJ. 67.  2009. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc. Natl. Acad. Sci. USA 106:2295–300 [Google Scholar]
  68. Hegarty MJ, Abbott RJ, Hiscock SJ. 68.  2012. Allopolyploid speciation in action: the origins and evolution of Senecio cambrensis. See Ref. 166 245–70
  69. Hegarty MJ, Barker GL, Brennan AC, Edwards KJ, Abbott RJ, Hiscock SJ. 69.  2008. Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio. Philos. Trans. R. Soc. Lond. B. 363:3055–69 [Google Scholar]
  70. Hegarty MJ, Barker GL, Wilson ID, Abbott RJ, Edwards KJ, Hiscock SJ. 70.  2006. Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Curr. Biol. 16:1652–59 [Google Scholar]
  71. Hirsch J, Lefort V, Vankersschaver M, Boualem A, Lucas A. 71.  et al. 2006. Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol. 140:1192–204 [Google Scholar]
  72. Hollister JD, Gaut BS. 72.  2009. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 19:1419–28 [Google Scholar]
  73. Hollister JD, Smith LM, Guo YL, Ott F, Weigel D, Gaut BS. 73.  2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl. Acad. Sci. USA 108:2322–27 [Google Scholar]
  74. Hovav R, Udall JA, Chaudhary B, Rapp R, Flagel L, Wendel JF. 74.  2008. Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proc. Natl. Acad. Sci. USA 105:6191–95 [Google Scholar]
  75. Hu G, Houston NL, Pathak D, Schmidt L, Thelen JJ, Wendel JF. 75.  2011. Genomically biased accumulation of seed storage proteins in allopolyploid cotton. Genetics 189:1103–15 [Google Scholar]
  76. Hu G, Koh J, Yoo MJ, Grupp K, Chen S, Wendel JF. 76.  2013. Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense. New Phytol. 200:570–82 [Google Scholar]
  77. Hudson CM, Puckett EE, Bekaert M, Pires JC, Conant GC. 77.  2011. Selection for higher gene copy number after different types of plant gene duplications. Genome Biol. Evol. 3:1369–80 [Google Scholar]
  78. Hughes AL. 78.  1994. The evolution of functionally novel proteins after gene duplication. Proc. Biol. Sci. 256:119–24 [Google Scholar]
  79. Ilut DC, Coate JE, Luciano AK, Owens TG, May GD. 79.  et al. 2012. A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-Seq in plant species. Am. J. Bot. 99:383–96 [Google Scholar]
  80. Irimia M, Rukov JL, Penny D, Garcia-Fernandez J, Vinther J, Roy SW. 80.  2008. Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. Mol. Biol. Evol. 25:375–82 [Google Scholar]
  81. Jackson S, Chen ZJ. 81.  2010. Genomic and expression plasticity of polyploidy. Curr. Opin. Plant Biol. 13:153–59 [Google Scholar]
  82. Jin L, Kryukov K, Clemente JC, Komiyama T, Suzuki Y. 82.  et al. 2008. The evolutionary relationship between gene duplication and alternative splicing. Gene 427:19–31 [Google Scholar]
  83. Joly S, Rauscher JT, Sherman-Broyles SL, Brown AHD, Doyle JJ. 83.  2004. Evolutionary dynamics and preferential expression of homeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial glycine allopolyploids. Mol. Biol. Evol. 21:1409–21 [Google Scholar]
  84. Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y. 84.  et al. 2012. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res. 40:2454–69 [Google Scholar]
  85. Kashkush K, Feldman M, Levy AA. 85.  2002. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160:1651–59 [Google Scholar]
  86. Kashkush K, Feldman M, Levy AA. 86.  2003. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 33:102–6 [Google Scholar]
  87. Kazan K. 87.  2003. Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged. Trends Plant Sci. 8:468–71 [Google Scholar]
  88. Kenton A, Parokonny AS, Gleba YY, Bennett MD. 88.  1993. Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics. Mol. Gen. Genet. 240:159–69 [Google Scholar]
  89. Kihara H, Ono T. 89.  1926. Chromosomenzahlen und Systematische Gruppierung der Rumex-Arten. Zeitschr. Zellf. Mikrosk. Anat. 4:475–81 [Google Scholar]
  90. Kim ED, Chen ZJ. 90.  2011. Unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression in response to abiotic and biotic stresses. PLOS ONE 6:e24251 [Google Scholar]
  91. Koh J, Chen S, Zhu N, Yu F, Soltis PS, Soltis DE. 91.  2012. Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents. New Phytol. 196:292–305 [Google Scholar]
  92. Koh J, Soltis PS, Soltis DE. 92.  2010. Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae). BMC Genomics 11:97 [Google Scholar]
  93. Kong F, Mao S, Jiang J, Wang J, Fang X, Wang Y. 93.  2011. Proteomic changes in newly synthesized Brassica napus allotetraploids and their early generations. Plant Mol. Biol. Rep. 29:927–35 [Google Scholar]
  94. Kovarik A, Matyasek R, Lim KY, Skalicka K, Koukalova B. 94.  et al. 2004. Concerted evolution of 18–5.8–26S rDNA repeats in Nicotiana allotetraploids. Biol. J. Linn. Soc. 82:615–25 [Google Scholar]
  95. Kraitshtein Z, Yaakov B, Khasdan V, Kashkush K. 95.  2010. Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat. Genetics 186:801–12 [Google Scholar]
  96. Kuwada Y. 96.  1911. Meiosis in the pollen mother cells of Zea mays L. Bot. Mag. Tokyo 25:163–81 [Google Scholar]
  97. Lashermes P, Paczek V, Trouslot P, Combes MC, Couturon E, Charrier A. 97.  2000. Single-locus inheritance in the allotetraploid Coffea arabica L. and interspecific hybrid C. arabica × C. canephora. J. Hered. 91:81–85 [Google Scholar]
  98. Leach LJ, Belfield EJ, Jiang C, Brown C, Mithani A, Harberd NP. 98.  2014. Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat. BMC Genomics 15:276 [Google Scholar]
  99. Lee HS, Chen ZJ. 99.  2001. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. USA 98:6753–58 [Google Scholar]
  100. Leitch IJ, Bennett MD. 100.  2004. Genome downsizing in polyploid plants. Biol. J. Linn. Soc. 82:651–63 [Google Scholar]
  101. Leon P, Arroyo A, Mackenzie S. 101.  1998. Nuclear control of plastid and mitochondrial development in higher plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49:453–80 [Google Scholar]
  102. Levin DA. 102.  1983. Polyploidy and novelty in flowering plants. Am. Nat. 122:1–25 [Google Scholar]
  103. Levin DA. 103.  2002. The Role of Chromosomal Change in Plant Evolution Oxford: Oxford Univ. Press
  104. Levy AA, Feldman M. 104.  2004. Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization. Biol. J. Linn. Soc. 82:607–13 [Google Scholar]
  105. Lewis WH. 105.  1980. Polyploidy in angiosperms: dicotyledons. Polyploidy: Biological Relevance WH Lewis 241–68 New York: Plenum Press [Google Scholar]
  106. Li JJ, Bickel PJ, Biggin MD. 106.  2014. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ. 2:e270 [Google Scholar]
  107. Li P, Ponnala L, Gandotra N, Wang L, Si Y. 107.  et al. 2010. The developmental dynamics of the maize leaf transcriptome. Nat. Genet. 42:1060–67 [Google Scholar]
  108. Li Q, Xiao G, Zhu YX. 108.  2014. Single-nucleotide resolution mapping of the Gossypium raimondii transcriptome reveals a new mechanism for alternative splicing of introns. Mol. Plant. 7:829–40
  109. Lim KY, Matyasek R, Kovarik A, Leitch AR. 109.  2004. Genome evolution in allotetraploid Nicotiana. Biol. J. Linn. Soc. 82:599–606 [Google Scholar]
  110. Liu B, Wendel JF. 110.  2003. Epigenetic phenomena and the evolution of plant allopolyploids. Mol. Phylogenet. Evol. 29:365–79 [Google Scholar]
  111. Lozano R, Ponce O, Ramirez M, Mostajo N, Orjeda G. 111.  2012. Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group Phureja. PLOS ONE 7:e34775 [Google Scholar]
  112. Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, Osborn T. 112.  2006. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol. 140:336–48 [Google Scholar]
  113. Lynch M, Force AG. 113.  2000. The origin of interspecific genomic incompatibility via gene duplication. Am. Nat. 156:590–605 [Google Scholar]
  114. Madlung A, Tyagi AP, Watson B, Jiang HM, Kagochi T. 114.  et al. 2005. Genomic changes in synthetic Arabidopsis polyploids. Plant J. 41:221–30 [Google Scholar]
  115. Marmagne A, Brabant P, Thiellement H, Alix K. 115.  2010. Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation. New Phytol. 186:216–27 [Google Scholar]
  116. Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M. 116.  2012. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 22:1184–95 [Google Scholar]
  117. Mayfield-Jones D, Washburn JD, Arias T, Edger PP, Pires JC, Conant GC. 117.  2013. Watching the grin fade: tracing the effects of polyploidy on different evolutionary time scales. Semin. Cell Dev. Biol. 24:320–31 [Google Scholar]
  118. McClintock B. 118.  1984. The significance of responses of the genome to challenge. Science 226:792–801 [Google Scholar]
  119. McGrath CL, Gout JF, Johri P, Doak TG, Lynch M. 119.  2014. Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Res. doi:10.1101/gr.173740.114
  120. McGrath C, Lynch M. 120.  2012. Evolutionary significance of whole-genome duplication. See Ref. 166 1–20
  121. Meng Y, Shao C, Ma X, Wang H. 121.  2013. Introns targeted by plant microRNAs: a possible novel mechanism of gene regulation. Rice 6:8 [Google Scholar]
  122. Mochida K, Yamazaki Y, Ogihara Y. 122.  2003. Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol. Genet. Genomics 270:371–77 [Google Scholar]
  123. Moghe GD, Hufnagel DE, Tang H, Xiao Y, Dworkin I. 123.  et al. 2014. Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species. Plant Cell 26:51925–37 [Google Scholar]
  124. Müntzing A. 124.  1936. The evolutionary significance of autopolyploidy. Hereditas 21:263–378 [Google Scholar]
  125. Murat F, Zhang R, Guizard S, Flores R, Armero A. 125.  et al. 2014. Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Genome Biol. Evol. 6:12–33 [Google Scholar]
  126. Nagaharu U. 126.  1935. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn. J. Bot. 7:389–452 [Google Scholar]
  127. Ng DW, Lu J, Chen ZJ. 127.  2012. Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility. Curr. Opin. Plant Biol. 15:154–61 [Google Scholar]
  128. Ng DW, Zhang C, Miller M, Shen Z, Briggs SP, Chen ZJ. 128.  2012. Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity 108:419–30 [Google Scholar]
  129. Ning K, Fermin D, Nesvizhskii AI. 129.  2012. Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. J. Proteome Res. 11:2261–71 [Google Scholar]
  130. Nyiko T, Sonkoly B, Merai Z, Benkovics AH, Silhavy D. 130.  2009. Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner. Plant Mol. Biol. 71:367–78 [Google Scholar]
  131. Ohno S. 131.  1970. Evolution by Gene Duplication New York: Springer-Verlag
  132. Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ. 132.  et al. 2003. Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19:141–47 [Google Scholar]
  133. Ownbey M. 133.  1950. Natural hybridization and amphiploidy in the genus Tragopogon. Am. J. Bot. 37:487–99 [Google Scholar]
  134. Ozkan H, Levy AA, Feldman M. 134.  2001. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13:1735–47 [Google Scholar]
  135. Ozkan H, Levy AA, Feldman M. 135.  2002. Rapid differentiation of homeologous chromosomes in newly-formed allopolyploid wheat. Isr. J. Plant Sci. 50:S65–76 [Google Scholar]
  136. Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien MA, Ainouche M. 136.  2009. Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol. 184:1003–15 [Google Scholar]
  137. Parkin IA, Gulden SM, Sharpe AG, Lukens L, Trick M. 137.  et al. 2005. Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171:765–81 [Google Scholar]
  138. Parkin IAP, Sharpe AG, Keith DJ, Lydiate DJ. 138.  1995. Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome 38:1122–31 [Google Scholar]
  139. Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, Estill JC. 139.  2006. Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet. 22:597–602 [Google Scholar]
  140. Pires JC, Zhao JW, Schranz ME, Leon EJ, Quijada PA. 140.  et al. 2004. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol. J. Linn. Soc. 82:675–88 [Google Scholar]
  141. Pontes O, Neves N, Silva M, Lewis MS, Madlung A. 141.  et al. 2004. Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc. Natl. Acad. Sci. USA 101:18240–45 [Google Scholar]
  142. Pumphrey M, Bai J, Laudencia-Chingcuanco D, Anderson O, Gill BS. 142.  2009. Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 181:1147–57 [Google Scholar]
  143. Qi B, Huang W, Zhu B, Zhong X, Guo J. 143.  et al. 2012. Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines. BMC Biol. 10:3 [Google Scholar]
  144. Rambani A, Page JT, Udall JA. 144.  2014. Polyploidy and the petal transcriptome of Gossypium. BMC Plant Biol. 14:3 [Google Scholar]
  145. Rapp RA, Udall JA, Wendel JF. 145.  2009. Genomic expression dominance in allopolyploids. BMC Biol. 7:18 [Google Scholar]
  146. Reddy AS, Marquez Y, Kalyna M, Barta A. 146.  2013. Complexity of the alternative splicing landscape in plants. Plant Cell 25:3657–83 [Google Scholar]
  147. Reddy AS, Rogers MF, Richardson DN, Hamilton M, Ben-Hur A. 147.  2012. Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Front. Plant Sci. 3:18 [Google Scholar]
  148. Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT. 148.  et al. 2014. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol. Evol. 6:559–71 [Google Scholar]
  149. Rhoades MM. 149.  1951. Duplicate genes in maize. Am. Nat. 85:105–10 [Google Scholar]
  150. Roulin A, Auer PL, Libault M, Schlueter J, Farmer A. 150.  et al. 2012. The fate of duplicated genes in a polyploid plant genome. Plant J. 73:143–53 [Google Scholar]
  151. Roux J, Robinson-Rechavi M. 151.  2011. Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication. Genome Res. 21:357–63 [Google Scholar]
  152. Sagasti S, Bernal M, Sancho D, del Castillo MB, Picorel R. 152.  2014. Regulation of the chloroplastic copper chaperone (CCS) and cuprozinc superoxide dismutase (CSD2) by alternative splicing and copper excess in Glycine max. Funct. Plant Biol. 41:144–55 [Google Scholar]
  153. Salmon A, Ainouche ML, Wendel JF. 153.  2005. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol. Ecol. 14:1163–75 [Google Scholar]
  154. Salse J, Bolot S, Throude M, Jouffe V, Piegu B. 154.  et al. 2008. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 20:11–24 [Google Scholar]
  155. Santos ME, Athanasiadis A, Leitao AB, DuPasquier L, Sucena E. 155.  2011. Alternative splicing and gene duplication in the evolution of the FoxP gene subfamily. Mol. Biol. Evol. 28:237–47 [Google Scholar]
  156. Schnable JC, Freeling M. 156.  2011. Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLOS ONE 6:e17855 [Google Scholar]
  157. Schnable JC, Freeling M. 157.  2012. Maize (Zea mays) as a model for studying the impact of gene and regulatory sequence loss following whole-genome duplication. See Ref. 166 137–45
  158. Schnable JC, Springer NM, Freeling M. 158.  2011. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. USA 108:4069–74 [Google Scholar]
  159. Sehrish T, Symonds VV, Soltis DE, Soltis PS, Tate JA. 159.  2014. Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids. BMC Genomics 15:701
  160. Seoighe C, Gehring C. 160.  2004. Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet. 20:461–64 [Google Scholar]
  161. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA. 161.  2001. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13:1749–59 [Google Scholar]
  162. Shi X, Ng DW, Zhang C, Comai L, Ye W, Chen ZJ. 162.  2012. Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids. Nat. Commun. 3:950 [Google Scholar]
  163. Soltis DE, Buggs RJA, Barbazuk WB, Chamala S, Chester M. 163.  et al. 2012. Rapid and repeated evolution in the early stages of polyploidy: genomic and cytogenetic studies of recent polyploidy in Tragopogon. See Ref. 166 271–92
  164. Soltis DE, Buggs RJA, Barbazuk WB, Schnable PS, Soltis PS. 164.  2009. On the origins of species: Does evolution repeat itself in polyploid populations of independent origin?. Cold Spring Harb. Symp. Quant. Biol. 74:215–23 [Google Scholar]
  165. Soltis DE, Soltis PS, Pires JC, Kovarik A, Tate JA. 165.  2004. Recent and recurrent polyploidy in Tragopogon (Asteraceae): genetic, genomic, and cytogenetic comparisons. Biol. J. Linn. Soc. 82:485–501 [Google Scholar]
  166. Soltis PS, Soltis DE. 166.  2012. Polyploidy and Genome Evolution Heidelberg, Ger.: Springer
  167. Song K, Lu P, Tang K, Osborn TC. 167.  1995. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. USA 92:7719–23 [Google Scholar]
  168. Stebbins GL. 168.  1950. Variation and Evolution in Plants New York: Columbia Univ. Press
  169. Su Z, Wang J, Yu J, Huang X, Gu X. 169.  2006. Evolution of alternative splicing after gene duplication. Genome Res. 16:182–89 [Google Scholar]
  170. Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V. 170.  et al. 2004. Close split of sorghum and maize genome progenitors. Genome Res. 14:1916–23 [Google Scholar]
  171. Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW. 171.  2012. Alternative splicing in plants: coming of age. Trends Plant Sci. 17:616–23 [Google Scholar]
  172. Szarzynska B, Sobkowiak L, Pant BD, Balazadeh S, Scheible WR. 172.  et al. 2009. Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs. Nucleic Acids Res. 37:3083–93 [Google Scholar]
  173. Talavera D, Vogel C, Orozco M, Teichmann SA, de la Cruz X. 173.  2007. The (in)dependence of alternative splicing and gene duplication. PLOS Comput. Biol. 3:e33 [Google Scholar]
  174. Terashima A, Takumi S. 174.  2009. Allopolyploidization reduces alternative splicing efficiency for transcripts of the wheat DREB2 homolog, WDREB2. Genome 52:100–5 [Google Scholar]
  175. Tian L, Li X, Ha M, Zhang C, Chen ZJ. 175.  2014. Genetic and epigenetic changes in a genomic region containing MIR172 in Arabidopsis allopolyploids and their progenitors. Heredity 112:207–14 [Google Scholar]
  176. Udall JA, Quijada PA, Osborn TC. 176.  2005. Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L. Genetics 169:967–79 [Google Scholar]
  177. Veitia RA, Bottani S, Birchler JA. 177.  2013. Gene dosage effects: nonlinearities, genetic interactions, and dosage compensation. Trends Genet. 29:385–93 [Google Scholar]
  178. Walters B, Lum G, Sablok G, Min XJ. 178.  2013. Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res. 20:163–71 [Google Scholar]
  179. Wang J, Tian L, Lee HS, Wei NE, Jiang H. 179.  et al. 2006. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507–17 [Google Scholar]
  180. Wang X, Wang H, Wang J, Sun R, Wu J. 180.  et al. 2011. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43:1035–39 [Google Scholar]
  181. Wang Z, Gerstein M, Snyder M. 181.  2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:57–63 [Google Scholar]
  182. Wei F, Coe E, Nelson W, Bharti AK, Engler F. 182.  et al. 2007. Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLOS Genet. 3:e123 [Google Scholar]
  183. Wendel JF, Cronn RC. 183.  2003. Polyploidy and the evolutionary history of cotton. Adv. Agron. 78:139–86 [Google Scholar]
  184. Wendel JF, Flagel LE, Adams KL. 184.  2012. Jeans, genes, and genomes: cotton as a model for studying polyploidy. See Ref. 166 181–207
  185. Wendel JF, Schnabel A, Seelanan T. 185.  1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA 92:280–84 [Google Scholar]
  186. Wolf JB. 186.  2009. Cytonuclear interactions can favor the evolution of genomic imprinting. Evolution 63:1364–71 [Google Scholar]
  187. Wolf JB, Hager R. 187.  2006. A maternal-offspring coadaptation theory for the evolution of genomic imprinting. PLOS Biol. 4:e380 [Google Scholar]
  188. Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X. 188.  2014. Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proc. Natl. Acad. Sci. USA 111:5283–88 [Google Scholar]
  189. Wu HP, Su YS, Chen HC, Chen YR, Wu CC. 189.  et al. 2014. Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. Genome Biol. 15:R10 [Google Scholar]
  190. Xiong Z, Gaeta RT, Pires JC. 190.  2011. Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc. Natl. Acad. Sci. USA 108:7908–13 [Google Scholar]
  191. Xu JH, Messing J. 191.  2008. Organization of the prolamin gene family provides insight into the evolution of the maize genome and gene duplications in grass species. Proc. Natl. Acad. Sci. USA 105:14330–35 [Google Scholar]
  192. Yan K, Liu P, Wu CA, Yang GD, Xu R. 192.  et al. 2012. Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana. Mol. Cell 48:521–31 [Google Scholar]
  193. Yang X, Zhang H, Li L. 193.  2012. Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis. Plant J. 70:421–31 [Google Scholar]
  194. Yoo MJ, Szadkowski E, Wendel JF. 194.  2013. Homoeolog expression bias and expression level dominance in allopolyploid cotton. Heredity 110:171–80 [Google Scholar]
  195. Zhang G, Guo G, Hu X, Zhang Y, Li Q. 195.  et al. 2010. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 20:646–54 [Google Scholar]
  196. Zhang PG, Huang SZ, Pin AL, Adams KL. 196.  2010. Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis. Mol. Biol. Evol. 27:1686–97 [Google Scholar]
  197. Zhang Z, Zhou L, Wang P, Liu Y, Chen X. 197.  et al. 2009. Divergence of exonic splicing elements after gene duplication and the impact on gene structures. Genome Biol. 10:R120 [Google Scholar]
  198. Zhou RC, Moshgabadi N, Adams KL. 198.  2011. Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids. Proc. Natl. Acad. Sci. USA 108:16122–27 [Google Scholar]
  199. Zhu W, Schlueter SD, Brendel V. 199.  2003. Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping. Plant Physiol. 132:469–84 [Google Scholar]
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Nonadditive Gene Expression in Polyploids
Annual Review of Genetics 48, 485 (2014); https://doi.org/10.1146/annurev-genet-120213-092159
/content/journals/10.1146/annurev-genet-120213-092159
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