Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1860, Issue 1, 2017, Pages 3-20

  Lehti Shiu, Melissa D ^a   Panchy, Nicholas ^b   Wang, Peipei ^a   Uygun, Sahra ^b   Shiu, Shin Han ^a,b  

^a Department of Plant Biology ^*  (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

Evolutionary conservation; Family expansion; Plant novelties; Retention mechanisms; Transcription factor domain families

Indexed keywords

PLANT DNA; TRANSCRIPTION FACTOR; DNA BINDING PROTEIN; PLANT PROTEIN;

AGRONOMIC TRAIT; CONTROLLED STUDY; DNA BINDING; DOMESTICATION; FAMILY SIZE; GENETIC CONSERVATION; MULTIGENE FAMILY; NONHUMAN; PLANT DEVELOPMENT; PLANT EVOLUTION; PLANT STRESS; PRIORITY JOURNAL; REVIEW; TRANSCRIPTION INITIATION; VIRIDIPLANTAE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PLANT;

DNA, PLANT; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; PLANT PROTEINS; PLANTS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 85004010418     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2016.08.005     Document Type: Review

References (350)

1. [1] Van Lijsebettens, M., Grasser, K.D., Transcript elongation factors: shaping transcriptomes after transcript initiation. Trends Plant Sci. 19 (2014), 717–726.
2. [2] Cheung, A.C.M., Cramer, P., A movie of RNA polymerase II transcription. Cell 149 (2012), 1431–1437.
3. [3] Hong, J.C., General Aspects of Plant Transcription Factor Families. Plant Transcription Factors, 2016, Elsevier, 35–56.
4. [4] Haag, J.R., Pikaard, C.S., Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat. Rev. Mol. Cell Biol. 12 (2011), 483–492.
5. [5] Wierzbicki, A.T., Haag, J.R., Pikaard, C.S., Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135 (2008), 635–648.
6. [6] Ariel, F., Romero-Barrios, N., Jégu, T., Benhamed, M., Crespi, M., Battles and hijacks: noncoding transcription in plants. Trends Plant Sci. 20 (2015), 362–371.
7. [7] Singh, K.B., Transcriptional regulation in plants: the importance of combinatorial control. Plant Physiol. 118 (1998), 1111–1120.
8. [8] Kaufmann, K., Pajoro, A., Angenent, G.C., Regulation of transcription in plants: mechanisms controlling developmental switches. Nat. Rev. Genet. 11 (2010), 830–842.
9. [9] Ikeuchi, M., Iwase, A., Sugimoto, K., Control of plant cell differentiation by histone modification and DNA methylation. Curr. Opin. Plant Biol. 28 (2015), 60–67.
10. [10] Du, J., Johnson, L.M., Jacobsen, S.E., Patel, D.J., DNA methylation pathways and their crosstalk with histone methylation. Nat. Rev. Mol. Cell Biol. 16 (2015), 519–532.
11. [11] Zhou, W., Zhu, Y., Dong, A., Shen, W.-H., Histone H2A/H2B chaperones: from molecules to chromatin-based functions in plant growth and development. Plant J. 83 (2015), 78–95.
12. [12] Wu, M.-F., Yamaguchi, N., Xiao, J., Bargmann, B., Estelle, M., Sang, Y., Wagner, D., Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. Elife, 4, 2015, e09269.
13. [13] Kagale, S., Rozwadowski, K., EAR motif-mediated transcriptional repression in plants: an underlying mechanism for epigenetic regulation of gene expression. Epigenetics 6 (2011), 141–146.
14. [14] Jing, Y., Sun, H., Yuan, W., Wang, Y., Li, Q., Liu, Y., Li, Y., Qian, W., SUVH2 and SUVH9 couple two essential steps for transcriptional gene silencing in Arabidopsis. Mol. Plant, 2016, 10.1016/j.molp.2016.05.006.
15. [15] Heo, J.B., Lee, Y.-S., Sung, S., Epigenetic regulation by long noncoding RNAs in plants. Chromosom. Res. 21 (2013), 685–693.
16. [16] Holoch, D., Moazed, D., RNA-mediated epigenetic regulation of gene expression. Nat. Rev. Genet. 16 (2015), 71–84.
17. [17] Rodriguez-Granados, N.Y., Ramirez-Prado, J.S., Veluchamy, A., Latrasse, D., Raynaud, C., Crespi, M., Ariel, F., Benhamed, M., Put your 3D glasses on: plant chromatin is on show. J. Exp. Bot. 67 (2016), 3205–3221.
18. [18] Wu, Z., Ietswaart, R., Liu, F., Yang, H., Howard, M., Dean, C., Quantitative regulation of FLC via coordinated transcriptional initiation and elongation. Proc. Natl. Acad. Sci. U. S. A. 113 (2016), 218–223.
19. [19] Proudfoot, N.J., Furger, A., Dye, M.J., Integrating mRNA processing with transcription. Cell 108 (2002), 501–512.
20. [20] Nagaya, S., Kawamura, K., Shinmyo, A., Kato, K., The HSP terminator of Arabidopsis thaliana increases gene expression in plant cells. Plant Cell Physiol. 51 (2010), 328–332.
21. [21] Guo, C., Spinelli, M., Liu, M., Li, Q.Q., Liang, C., A genome-wide study of “Non-3UTR” polyadenylation sites in Arabidopsis thaliana. Sci. Rep., 6, 2016, 28060.
22. [22] Proudfoot, N.J., Transcriptional termination in mammals: stopping the RNA polymerase II juggernaut. Science, 352, 2016 (aad9926).
23. [23] Latchman, D.S., Eukaryotic transcription factors. Biochem. J. 270 (1990), 281–289.
24. [24] Latchman, D.S., Transcription factors: an overview. Int. J. Biochem. Cell Biol. 29 (1997), 1305–1312.
25. [25] Gill, G., Regulation of the initiation of eukaryotic transcription. Essays Biochem. 37 (2001), 33–43.
26. [26] Narlikar, G.J., Fan, H.-Y., Kingston, R.E., Cooperation between complexes that regulate chromatin structure and transcription. Cell 108 (2002), 475–487.
27. [27] Benfey, P.N., Toward a systems analysis of the root. Cold Spring Harb. Symp. Quant. Biol. 77 (2012), 91–96.
28. [28] Soltis, D.E., Soltis, P.S., Albert, V.A., Oppenheimer, D.G., dePamphilis, C.W., Ma, H., Frohlich, M.W., Theissen, G., Floral genome project research group, missing links: the genetic architecture of flowers [correction of flower] and floral diversification. Trends Plant Sci. 7 (2002), 22–31 (dicussion 31–4).
29. [29] Coen, E.S., Meyerowitz, E.M., The war of the whorls: genetic interactions controlling flower development. Nature 353 (1991), 31–37.
30. [30] Nakai, Y., Nakahira, Y., Sumida, H., Takebayashi, K., Nagasawa, Y., Yamasaki, K., Akiyama, M., Ohme-Takagi, M., Fujiwara, S., Shiina, T., Mitsuda, N., Fukusaki, E., Kubo, Y., Sato, M.H., Vascular plant one-zinc-finger protein 1/2 transcription factors regulate abiotic and biotic stress responses in Arabidopsis. Plant J. 73 (2013), 761–775.
31. [31] Nakashima, K., Takasaki, H., Mizoi, J., Shinozaki, K., Yamaguchi-Shinozaki, K., NAC transcription factors in plant abiotic stress responses. Biochim. Biophys. Acta 1819 (2012), 97–103.
32. [32] Singh, K., Foley, R.C., Oñate-Sánchez, L., Transcription factors in plant defense and stress responses. Curr. Opin. Plant Biol. 5 (2002), 430–436.
33. [33] Jin, H., Martin, C., Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41 (1999), 577–585.
34. [34] Gendron, J.M., Pruneda-Paz, J.L., Doherty, C.J., Gross, A.M., Kang, S.E., Kay, S.A., Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proc. Natl. Acad. Sci. U. S. A. 109 (2012), 3167–3172.
35. [35] Nader, N., Chrousos, G.P., Kino, T., Circadian rhythm transcription factor CLOCK regulates the transcriptional activity of the glucocorticoid receptor by acetylating its hinge region lysine cluster: potential physiological implications. FASEB J. 23 (2009), 1572–1583.
36. [36] Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, I., Giakountis, A., Farrona, S., Gissot, L., Turnbull, C., Coupland, G., FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316 (2007), 1030–1033.
37. [37] Bastías, A., Yañez, M., Osorio, S., Arbona, V., Gómez-Cadenas, A., Fernie, A.R., Casaretto, J.A., The transcription factor AREB1 regulates primary metabolic pathways in tomato fruits. J. Exp. Bot. 65 (2014), 2351–2363.
38. [38] Kim, W.-C., Ko, J.-H., Han, K.-H., Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis. Plant Mol. Biol. 78 (2012), 489–501.
39. [39] Taylor-Teeples, M., Lin, L., de Lucas, M., Turco, G., Toal, T.W., Gaudinier, A., Young, N.F., Trabucco, G.M., Veling, M.T., Lamothe, R., Handakumbura, P.P., Xiong, G., Wang, C., Corwin, J., Tsoukalas, A., Zhang, L., Ware, D., Pauly, M., Kliebenstein, D.J., Dehesh, K., Tagkopoulos, I., Breton, G., Pruneda-Paz, J.L., Ahnert, S.E., Kay, S.A., Hazen, S.P., Brady, S.M., An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature 517 (2015), 571–575.
40. [40] Della Pina, S., Souer, E., Koes, R., Arguments in the evo-devo debate: say it with flowers!. J. Exp. Bot. 65 (2014), 2231–2242.
41. [41] Riechmann, J.L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O.J., Samaha, R.R., Creelman, R., Pilgrim, M., Broun, P., Zhang, J.Z., Ghandehari, D., Sherman, B.K., Yu, G., Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290 (2000), 2105–2110.
42. [42] Mitsuda, N., Ohme-Takagi, M., Functional analysis of transcription factors in Arabidopsis. Plant Cell Physiol. 50 (2009), 1232–1248.
43. [43] Yamasaki, K., Kigawa, T., Seki, M., Shinozaki, K., Yokoyama, S., DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. Trends Plant Sci. 18 (2013), 267–276.
44. [44] de Mendoza, A., Sebé-Pedrós, A., Šestak, M.S., Matejcic, M., Torruella, G., Domazet-Loso, T., Ruiz-Trillo, I., Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proc. Natl. Acad. Sci. U. S. A. 110 (2013), E4858–E4866.
45. [45] Franco-Zorrilla, J.M., López-Vidriero, I., Carrasco, J.L., Godoy, M., Vera, P., Solano, R., DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc. Natl. Acad. Sci. U. S. A. 111 (2014), 2367–2372.
46. [46] Riaño-Pachón, D.M., Ruzicic, S., Dreyer, I., Mueller-Roeber, B., PlnTFDB: an integrative plant transcription factor database. BMC Bioinform., 8, 2007, 42.
47. [47] Richardt, S., Lang, D., Reski, R., Frank, W., Rensing, S.A., PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol. 143 (2007), 1452–1466.
48. [48] Jin, J., Zhang, H., Kong, L., Gao, G., Luo, J., PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 42 (2014), D1182–D1187.
49. [49] Kejnovsky, E., Leitch, I.J., Leitch, A.R., Contrasting evolutionary dynamics between angiosperm and mammalian genomes. Trends Ecol. Evol. 24 (2009), 572–582.
50. [50] Murat, F., Van de Peer, Y., Salse, J., Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. Genome Biol. Evol. 4 (2012), 917–928.
51. [51] Blanc, G., Wolfe, K.H., Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16 (2004), 1679–1691.
52. [52] Seoighe, C., Gehring, C., Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet. 20 (2004), 461–464.
53. [53] Shiu, S.-H., Shih, M.-C., Li, W.-H., Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol. 139 (2005), 18–26.
54. [54] Jiang, W.-K., Liu, Y.-L., Xia, E.-H., Gao, L.-Z., Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants. Plant Physiol. 161 (2013), 1844–1861.
55. [55] Kim, S., Soltis, P.S., Wall, K., Soltis, D.E., Phylogeny and domain evolution in the APETALA2-like gene family. Mol. Biol. Evol. 23 (2006), 107–120.
56. [56] Mizoi, J., Shinozaki, K., Yamaguchi-Shinozaki, K., AP2/ERF family transcription factors in plant abiotic stress responses. Biochim. Biophys. Acta 1819 (2012), 86–96.
57. [57] Shan, H., Zahn, L., Guindon, S., Wall, P.K., Kong, H., Ma, H., DePamphilis, C.W., Leebens-Mack, J., Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. Mol. Biol. Evol. 26 (2009), 2229–2244.
58. [58] Gramzow, L., Ritz, M.S., Theissen, G., On the origin of MADS-domain transcription factors. Trends Genet. 26 (2010), 149–153.
59. [59] Feller, A., Machemer, K., Braun, E.L., Grotewold, E., Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J. 66 (2011), 94–116.
60. [60] Du, H., Liang, Z., Zhao, S., Nan, M.-G., Tran, L.-S.P., Lu, K., Huang, Y.-B., Li, J.-N., The evolutionary history of R2R3-MYB proteins across 50 eukaryotes: new insights into subfamily classification and expansion. Sci. Rep., 5, 2015, 11037.
61. [61] Qin, Y., Ma, X., Yu, G., Wang, Q., Wang, L., Kong, L., Kim, W., Wang, H.W., Evolutionary history of trihelix family and their functional diversification. DNA Res. 21 (2014), 499–510.
62. [62] Mentink, R.A., Tsiantis, M., From limbs to leaves: common themes in evolutionary diversification of organ form. Front. Genet., 6, 2015, 284.
63. [63] Albert, N.W., Davies, K.M., Schwinn, K.E., Gene regulation networks generate diverse pigmentation patterns in plants. Plant Signal. Behav., 9, 2014, e29526.
64. [64] Nardmann, J., Werr, W., The evolution of plant regulatory networks: what Arabidopsis cannot say for itself. Curr. Opin. Plant Biol. 10 (2007), 653–659.
65. [65] Liu, L., White, M.J., MacRae, T.H., Transcription factors and their genes in higher plants functional domains, evolution and regulation. Eur. J. Biochem. 262 (1999), 247–257.
66. [66] Han, X., Kumar, D., Chen, H., Wu, S., Kim, J.-Y., Transcription factor-mediated cell-to-cell signalling in plants. J. Exp. Bot. 65 (2014), 1737–1749.
67. [67] Laloum, T., De Mita, S., Gamas, P., Baudin, M., Niebel, A., CCAAT-box binding transcription factors in plants: Y so many?. Trends Plant Sci. 18 (2013), 157–166.
68. [68] Gonzalez, D.H., Plant Transcription Factors: Evolutionary, Structural and Functional Aspects. 2015, Academic Press.
69. [69] Guo, A.-Y., Chen, X., Gao, G., Zhang, H., Zhu, Q.-H., Liu, X.-C., Zhong, Y.-F., Gu, X., He, K., Luo, J., PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res. 36 (2008), D966–D969.
70. [70] Lang, D., Weiche, B., Timmerhaus, G., Richardt, S., Riaño-Pachón, D.M., Corrêa, L.G.G., Reski, R., Mueller-Roeber, B., Rensing, S.A., Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol. Evol. 2 (2010), 488–503.
71. [71] Nagata, T., Toshifumi, N., Aeni, H.-S., Shoshi, K., The evolutionary diversification of genes that encode transcription factor proteins in plants. Plant Transcription Factors, 2016, 73–97.
72. [72] Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G.A., Tate, J., Bateman, A., The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44 (2016), D279–D285.
73. [73] Burki, F., The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harb. Perspect. Biol., 6, 2014, a016147.
74. [74] Weston, K., Myb proteins in life, death and differentiation. Curr. Opin. Genet. Dev. 8 (1998), 76–81.
75. [75] Fang, Z.H., Han, Z.C., The transcription factor E2F: a crucial switch in the control of homeostasis and tumorigenesis. Histol. Histopathol. 21 (2006), 403–413.
76. [76] Ledent, V., Vervoort, M., The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Res. 11 (2001), 754–770.
77. [77] Kortschak, R.D., Tucker, P.W., Saint, R., ARID proteins come in from the desert. Trends Biochem. Sci. 25 (2000), 294–299.
78. [78] Benatti, P., Dolfini, D., Viganò, A., Ravo, M., Weisz, A., Imbriano, C., Specific inhibition of NF-Y subunits triggers different cell proliferation defects. Nucleic Acids Res. 39 (2011), 5356–5368.
79. [79] Caretti, G., Salsi, V., Vecchi, C., Imbriano, C., Mantovani, R., Dynamic recruitment of NF-Y and histone acetyltransferases on cell-cycle promoters. J. Biol. Chem. 278 (2003), 30435–30440.
80. [80] Deed, R.W., Hara, E., Atherton, G.T., Peters, G., Norton, J.D., Regulation of Id3 cell cycle function by Cdk-2-dependent phosphorylation. Mol. Cell. Biol. 17 (1997), 6815–6821.
81. [81] Rövekamp, M., Bowman, J.L., Grossniklaus, U., Marchantia MpRKD regulates the gametophyte-sporophyte transition by keeping egg cells quiescent in the absence of fertilization. Curr. Biol. 26 (2016), 1782–1789.
82. [82] Koi, S., Hisanaga, T., Sato, K., Shimamura, M., Yamato, K.T., Ishizaki, K., Kohchi, T., Nakajima, K., An evolutionarily conserved plant RKD factor controls germ cell differentiation. Curr. Biol. 26 (2016), 1775–1781.
83. [83] Lin, H., Goodenough, U.W., Gametogenesis in the Chlamydomonas reinhardtii minus mating type is controlled by two genes, MID and MTD1. Genetics 176 (2007), 913–925.
84. [84] Ferris, P.J., Goodenough, U.W., Mating type in Chlamydomonas is specified by mid, the minus-dominance gene. Genetics 146 (1997), 859–869.
85. [85] Kanhere, A., Bansal, M., Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. Nucleic Acids Res. 33 (2005), 3165–3175.
86. [86] Struhl, K., Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98 (1999), 1–4.
87. [87] Schrumpfová, P.P., Fojtová, M., Mokroš, P., Grasser, K.D., Fajkus, J., Role of HMGB proteins in chromatin dynamics and telomere maintenance in Arabidopsis thaliana. Curr. Protein Pept. Sci. 12 (2011), 105–111.
88. [88] Stros, M., Launholt, D., Grasser, K.D., The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins. Cell. Mol. Life Sci. 64 (2007), 2590–2606.
89. [89] Cai, Y., Jin, J., Florens, L., Swanson, S.K., Kusch, T., Li, B., Workman, J.L., Washburn, M.P., Conaway, R.C., Conaway, J.W., The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes. J. Biol. Chem. 280 (2005), 13665–13670.
90. [90] Jin, S., Scotto, K.W., Transcriptional regulation of the MDR1 gene by histone acetyltransferase and deacetylase is mediated by NF-Y. Mol. Cell. Biol. 18 (1998), 4377–4384.
91. [91] Linhoff, M.W., Wright, K.L., Ting, J.P., CCAAT-binding factor NF-Y and RFX are required for in vivo assembly of a nucleoprotein complex that spans 250 base pairs: the invariant chain promoter as a model. Mol. Cell. Biol. 17 (1997), 4589–4596.
92. [92] Scazzocchio, C., The fungal GATA factors. Curr. Opin. Microbiol. 3 (2000), 126–131.
93. [93] Pearson, J.C., Lemons, D., McGinnis, W., Modulating Hox gene functions during animal body patterning. Nat. Rev. Genet. 6 (2005), 893–904.
94. [94] Ahn, S.G., Liu, P.C., Klyachko, K., Morimoto, R.I., Thiele, D.J., The loop domain of heat shock transcription factor 1 dictates DNA-binding specificity and responses to heat stress. Genes Dev. 15 (2001), 2134–2145.
95. [95] Deng, X., Yang, J., Wu, X., Li, Y., Fei, X., A C2H2 zinc finger protein FEMU2 is required for fox1 expression in Chlamydomonas reinhardtii. PLoS One, 9, 2014, e112977.
96. [96] Hai, T., Wolfgang, C.D., Marsee, D.K., Allen, A.E., Sivaprasad, U., ATF3 and stress responses. Gene Expr. 7 (1999), 321–335.
97. [97] Du, H., Zhang, L., Liu, L., Tang, X.-F., Yang, W.-J., Wu, Y.-M., Huang, Y.-B., Tang, Y.-X., Biochemical and molecular characterization of plant MYB transcription factor family. Biochemistry 74 (2009), 1–11.
98. [98] Deppmann, C.D., Alvania, R.S., Taparowsky, E.J., Cross-species annotation of basic leucine zipper factor interactions: insight into the evolution of closed interaction networks. Mol. Biol. Evol. 23 (2006), 1480–1492.
99. [99] Matuoka, K., Chen, K.Y., Nuclear factor Y (NF-Y) and cellular senescence. Exp. Cell Res. 253 (1999), 365–371.
100. [100] Finkler, A., Ashery-Padan, R., Fromm, H., CAMTAs: calmodulin-binding transcription activators from plants to human. FEBS Lett. 581 (2007), 3893–3898.
101. [101] Bottomley, M.J., Collard, M.W., Huggenvik, J.I., Liu, Z., Gibson, T.J., Sattler, M., The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation. Nat. Struct. Biol. 8 (2001), 626–633.
102. [102] Peterson, P., Org, T., Rebane, A., Transcriptional regulation by AIRE: molecular mechanisms of central tolerance. Nat. Rev. Immunol. 8 (2008), 948–957.
103. [103] Carles, C.C., Fletcher, J.C., The SAND domain protein ULTRAPETALA1 acts as a trithorax group factor to regulate cell fate in plants. Genes Dev. 23 (2009), 2723–2728.
104. [104] Carles, C.C., Choffnes-Inada, D., Reville, K., Lertpiriyapong, K., Fletcher, J.C., ULTRAPETALA1 encodes a SAND domain putative transcriptional regulator that controls shoot and floral meristem activity in Arabidopsis. Development 132 (2005), 897–911.
105. [105] Carles, C.C., Lertpiriyapong, K., Reville, K., Fletcher, J.C., The ULTRAPETALA1 gene functions early in Arabidopsis development to restrict shoot apical meristem activity and acts through WUSCHEL to regulate floral meristem determinacy. Genetics 167 (2004), 1893–1903.
106. [106] Monfared, M.M., Carles, C.C., Rossignol, P., Pires, H.R., Fletcher, J.C., The ULT1 and ULT2 trxG genes play overlapping roles in Arabidopsis development and gene regulation. Mol. Plant 6 (2013), 1564–1579.
107. [107] Ashraf, N., Jain, D., Vishwakarma, R.A., Identification, cloning and characterization of an ultrapetala transcription factor CsULT1 from Crocus: a novel regulator of apocarotenoid biosynthesis. BMC Plant Biol., 15, 2015, 25.
108. [108] Painter, H.J., Campbell, T.L., Llinás, M., The Apicomplexan AP2 family: integral factors regulating Plasmodium development. Mol. Biochem. Parasitol. 176 (2011), 1–7.
109. [109] Ha, C.M., Jun, J.H., Fletcher, J.C., Control of Arabidopsis leaf morphogenesis through regulation of the YABBY and KNOX families of transcription factors. Genetics 186 (2010), 197–206.
110. [110] Cong, B., Barrero, L.S., Tanksley, S.D., Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat. Genet. 40 (2008), 800–804.
111. [111] Dai, M., Hu, Y., Zhao, Y., Zhou, D.-X., Regulatory networks involving YABBY genes in rice shoot development. Plant Signal. Behav. 2 (2007), 399–400.
112. [112] Lee, J.-Y., Baum, S.F., Alvarez, J., Patel, A., Chitwood, D.H., Bowman, J.L., Activation of CRABS CLAW in the nectaries and carpels of Arabidopsis. Plant Cell 17 (2005), 25–36.
113. [113] Lin, Z., Li, X., Shannon, L.M., Yeh, C.-T., Wang, M.L., Bai, G., Peng, Z., Li, J., Trick, H.N., Clemente, T.E., Doebley, J., Schnable, P.S., Tuinstra, M.R., Tesso, T.T., White, F., Yu, J., Parallel domestication of the Shattering1 genes in cereals. Nat. Genet. 44 (2012), 720–724.
114. [114] Dai, M., Zhao, Y., Ma, Q., Hu, Y., Hedden, P., Zhang, Q., Zhou, D.-X., The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism. Plant Physiol. 144 (2007), 121–133.
115. [115] Eulgem, T., Rushton, P.J., Robatzek, S., Somssich, I.E., The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5 (2000), 199–206.
116. [116] Cappadocia, L., Maréchal, A., Parent, J.-S., Lepage, E., Sygusch, J., Brisson, N., Crystal structures of DNA-Whirly complexes and their role in Arabidopsis organelle genome repair. Plant Cell 22 (2010), 1849–1867.
117. [117] Maréchal, A., Parent, J.-S., Véronneau-Lafortune, F., Joyeux, A., Lang, B.F., Brisson, N., Whirly proteins maintain plastid genome stability in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 106 (2009), 14693–14698.
118. [118] Prikryl, J., Watkins, K.P., Friso, G., van Wijk, K.J., Barkan, A., A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis. Nucleic Acids Res. 36 (2008), 5152–5165.
119. [119] Yoo, H.H., Kwon, C., Lee, M.M., Chung, I.K., Single-stranded DNA binding factor AtWHY1 modulates telomere length homeostasis in Arabidopsis. Plant J. 49 (2007), 442–451.
120. [120] Desveaux, D., Subramaniam, R., Després, C., Mess, J.-N., Lévesque, C., Fobert, P.R., Dangl, J.L., Brisson, N., A “Whirly” transcription factor is required for salicylic acid-dependent disease resistance in Arabidopsis. Dev. Cell 6 (2004), 229–240.
121. [121] Miao, Y., Jiang, J., Ren, Y., Zhao, Z., The single-stranded DNA-binding protein WHIRLY1 represses WRKY53 expression and delays leaf senescence in a developmental stage-dependent manner in Arabidopsis. Plant Physiol. 163 (2013), 746–756.
122. [122] Licausi, F., Ohme-Takagi, M., Perata, P., APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs. New Phytol. 199 (2013), 639–649.
123. [123] Yuda, M., Iwanaga, S., Shigenobu, S., Mair, G.R., Janse, C.J., Waters, A.P., Kato, T., Kaneko, I., Identification of a transcription factor in the mosquito-invasive stage of malaria parasites. Mol. Microbiol. 71 (2009), 1402–1414.
124. [124] Flueck, C., Bartfai, R., Niederwieser, I., Witmer, K., Alako, B.T.F., Moes, S., Bozdech, Z., Jenoe, P., Stunnenberg, H.G., Voss, T.S., A major role for the Plasmodium falciparum ApiAP2 protein PfSIP2 in chromosome end biology. PLoS Pathog., 6, 2010, e1000784.
125. [125] Radke, J.B., Lucas, O., De Silva, E.K., Ma, Y., Sullivan, W.J. Jr., Weiss, L.M., Llinas, M., White, M.W., ApiAP2 transcription factor restricts development of the Toxoplasma tissue cyst. Proc. Natl. Acad. Sci. U. S. A. 110 (2013), 6871–6876.
126. [126] Golz, J.F., Hudson, A., Plant development: YABBYs claw to the fore. Curr. Biol. 9 (1999), R861–R863.
127. [127] Desveaux, D., Allard, J., Brisson, N., Sygusch, J., A new family of plant transcription factors displays a novel ssDNA-binding surface. Nat. Struct. Biol. 9 (2002), 512–517.
128. [128] Rinerson, C.I., Rabara, R.C., Tripathi, P., Shen, Q.J., Rushton, P.J., The evolution of WRKY transcription factors. BMC Plant Biol., 15, 2015, 66.
129. [129] Wessler, S.R., Homing into the origin of the AP2 DNA binding domain. Trends Plant Sci. 10 (2005), 54–56.
130. [130] McCarty, D.R., Hattori, T., Carson, C.B., Vasil, V., Lazar, M., Vasil, I.K., The Viviparous-1 developmental gene of maize encodes a novel transcriptional activator. Cell 66 (1991), 895–905.
131. [131] Swaminathan, K., Peterson, K., Jack, T., The plant B3 superfamily. Trends Plant Sci. 13 (2008), 647–655.
132. [132] Kagaya, Y., Ohmiya, K., Hattori, T., RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res. 27 (1999), 470–478.
133. [133] Jin, J., He, K., Tang, X., Li, Z., Lv, L., Zhao, Y., Luo, J., Gao, G., An Arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors. Mol. Biol. Evol. 32 (2015), 1767–1773.
134. [134] Yanagisawa, S., Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol. 45 (2004), 386–391.
135. [135] Yanagisawa, S., Dof DNA-binding domains of plant transcription factors contribute to multiple protein-protein interactions. Eur. J. Biochem. 250 (1997), 403–410.
136. [136] Yanagisawa, S., A novel DNA-binding domain that may form a single zinc finger motif. Nucleic Acids Res. 23 (1995), 3403–3410.
137. [137] Nagano, Y., Furuhashi, H., Inaba, T., Sasaki, Y., A novel class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. Nucleic Acids Res. 29 (2001), 4097–4105.
138. [138] Klein, J., Saedler, H., Huijser, P., A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol. Gen. Genet. 250 (1996), 7–16.
139. [139] van der Knaap, E., Kim, J.H., Kende, H., A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth. Plant Physiol. 122 (2000), 695–704.
140. [140] Chevalier, F., Perazza, D., Laporte, F., Le Hénanff, G., Hornitschek, P., Bonneville, J.-M., Herzog, M., Vachon, G., GeBP and GeBP-like proteins are noncanonical leucine-zipper transcription factors that regulate cytokinin response in Arabidopsis. Plant Physiol. 146 (2008), 1142–1154.
141. [141] Capella, M., Matías, C., Ribone, P.A., Arce, A.L., Chan, R.L., Homeodomain–leucine zipper transcription factors: structural features of these proteins, unique to plants. Plant Transcription Factors, 2016, 113–126.
142. [142] Rubin, G., Tohge, T., Matsuda, F., Saito, K., Scheible, W.-R., Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. Plant Cell 21 (2009), 3567–3584.
143. [143] Fridborg, I., Kuusk, S., Robertson, M., Sundberg, E., The Arabidopsis protein SHI represses gibberellin responses in Arabidopsis and barley. Plant Physiol. 127 (2001), 937–948.
144. [144] Kropat, J., Tottey, S., Birkenbihl, R.P., Depège, N., Huijser, P., Merchant, S., A regulator of nutritional copper signaling in Chlamydomonas is an SBP domain protein that recognizes the GTAC core of copper response element. Proc. Natl. Acad. Sci. U. S. A. 102 (2005), 18730–18735.
145. [145] Yamasaki, H., Hayashi, M., Fukazawa, M., Kobayashi, Y., Shikanai, T., SQUAMOSA promoter binding protein-like7 is a central regulator for copper homeostasis in Arabidopsis. Plant Cell 21 (2009), 347–361.
146. [146] Li, S., The Arabidopsis thaliana TCP transcription factors: a broadening horizon beyond development. Plant Signal. Behav., 10, 2015, e1044192.
147. [147] Romanel, E.A.C., Schrago, C.G., Couñago, R.M., Russo, C.A.M., Alves-Ferreira, M., Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification. PLoS One, 4, 2009, e5791.
148. [148] Shigyo, M., Tabei, N., Yoneyama, T., Yanagisawa, S., Evolutionary processes during the formation of the plant-specific Dof transcription factor family. Plant Cell Physiol. 48 (2007), 179–185.
149. [149] Riese, M., Zobell, O., Saedler, H., Huijser, P., SBP-domain transcription factors as possible effectors of cryptochrome-mediated blue light signalling in the moss Physcomitrella patens. Planta 227 (2008), 505–515.
150. [150] Olsen, A.N., Ernst, H.A., Leggio, L.L., Skriver, K., NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci. 10 (2005), 79–87.
151. [151] Matsumura, Y., Iwakawa, H., Machida, Y., Machida, C., Characterization of genes in the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members. Plant J. 58 (2009), 525–537.
152. [152] Bolle, C., The role of GRAS proteins in plant signal transduction and development. Planta 218 (2004), 683–692.
153. [153] Siriwardana, N.S., Lamb, R.S., The poetry of reproduction: the role of LEAFY in Arabidopsis thaliana flower formation. Int. J. Dev. Biol. 56 (2012), 207–221.
154. [154] Yamaguchi, A., Wu, M.-F., Yang, L., Wu, G., Poethig, R.S., Wagner, D., The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1. Dev. Cell 17 (2009), 268–278.
155. [155] Wei, B., Zhang, J., Pang, C., Yu, H., Guo, D., Jiang, H., Ding, M., Chen, Z., Tao, Q., Gu, H., Qu, L.-J., Qin, G., The molecular mechanism of sporocyteless/nozzle in controlling Arabidopsis ovule development. Cell Res. 25 (2015), 121–134.
156. [156] Guo, A.-Y., Zhu, Q.-H., Gu, X., Ge, S., Yang, J., Luo, J., Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family. Gene 418 (2008), 1–8.
157. [157] Binder, B.M., Walker, J.M., Gagne, J.M., Emborg, T.J., Hemmann, G., Bleecker, A.B., Vierstra, R.D., The Arabidopsis EIN3 binding F-Box proteins EBF1 and EBF2 have distinct but overlapping roles in ethylene signaling. Plant Cell 19 (2007), 509–523.
158. [158] Li, L., Deng, X.W., It runs in the family: regulation of brassinosteroid signaling by the BZR1-BES1 class of transcription factors. Trends Plant Sci. 10 (2005), 266–268.
159. [159] Kaló, P., Gleason, C., Edwards, A., Marsh, J., Mitra, R.M., Hirsch, S., Jakab, J., Sims, S., Long, S.R., Rogers, J., Kiss, G.B., Downie, J.A., Oldroyd, G.E.D., Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators. Science 308 (2005), 1786–1789.
160. [160] Fode, B., Siemsen, T., Thurow, C., Weigel, R., Gatz, C., The Arabidopsis GRAS protein SCL14 interacts with class II TGA transcription factors and is essential for the activation of stress-inducible promoters. Plant Cell 20 (2008), 3122–3135.
161. [161] Zhang, D., Iyer, L.M., Aravind, L., Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms. Bioinformatics 28 (2012), 2407–2411.
162. [162] Kurokawa, H., Motohashi, H., Sueno, S., Kimura, M., Takagawa, H., Kanno, Y., Yamamoto, M., Tanaka, T., Structural basis of alternative DNA recognition by Maf transcription factors. Mol. Cell. Biol. 29 (2009), 6232–6244.
163. [163] Liang, H., Olejniczak, E.T., Mao, X., Nettesheim, D.G., Yu, L., Thompson, C.B., Fesik, S.W., The secondary structure of the ets domain of human Fli-1 resembles that of the helix-turn-helix DNA-binding motif of the Escherichia coli catabolite gene activator protein. Proc. Natl. Acad. Sci. U. S. A. 91 (1994), 11655–11659.
164. [164] Häcker, U., Grossniklaus, U., Gehring, W.J., Jäckle, H., Developmentally regulated Drosophila gene family encoding the fork head domain. Proc. Natl. Acad. Sci. U. S. A. 89 (1992), 8754–8758.
165. [165] van der Horst, A., Burgering, B.M.T., Stressing the role of FoxO proteins in lifespan and disease. Nat. Rev. Mol. Cell Biol. 8 (2007), 440–450.
166. [166] Wang, J.-J., Qiu, L., Cai, Q., Ying, S.-H., Feng, M.-G., Transcriptional control of fungal cell cycle and cellular events by Fkh2, a forkhead transcription factor in an insect pathogen. Sci. Rep., 5, 2015, 10108.
167. [167] Oikawa, T., Yamada, T., Molecular biology of the Ets family of transcription factors. Gene 303 (2003), 11–34.
168. [168] Shelest, E., Transcription factors in fungi. FEMS Microbiol. Lett. 286 (2008), 145–151.
169. [169] Turner, R.B., Smith, D.L., Zawrotny, M.E., Summers, M.F., Posewitz, M.C., Winge, D.R., Solution structure of a zinc domain conserved in yeast copper-regulated transcription factors. Nat. Struct. Biol. 5 (1998), 551–555.
170. [170] 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.
171. [171] Rensing, S.A., Lang, D., Zimmer, A.D., Terry, A., Salamov, A., Shapiro, H., Nishiyama, T., Perroud, P.-F., Lindquist, E.A., Kamisugi, Y., Tanahashi, T., Sakakibara, K., Fujita, T., Oishi, K., Shin-I, T., Kuroki, Y., Toyoda, A., Suzuki, Y., Hashimoto, S.-I., Yamaguchi, K., Sugano, S., Kohara, Y., Fujiyama, A., Anterola, A., Aoki, S., Ashton, N., Barbazuk, W.B., Barker, E., Bennetzen, J.L., Blankenship, R., Cho, S.H., Dutcher, S.K., Estelle, M., Fawcett, J.A., Gundlach, H., Hanada, K., Heyl, A., Hicks, K.A., Hughes, J., Lohr, M., Mayer, K., Melkozernov, A., Murata, T., Nelson, D.R., Pils, B., Prigge, M., Reiss, B., Renner, T., Rombauts, S., Rushton, P.J., Sanderfoot, A., Schween, G., Shiu, S.-H., Stueber, K., Theodoulou, F.L., Tu, H., Van de Peer, Y., Verrier, P.J., Waters, E., Wood, A., Yang, L., Cove, D., Cuming, A.C., Hasebe, M., Lucas, S., Mishler, B.D., Reski, R., Grigoriev, I.V., Quatrano, R.S., Boore, J.L., The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319 (2008), 64–69.
172. [172] Sanderson, M.J., Thorne, J.L., Wikström, N., Bremer, K., Molecular evidence on plant divergence times. Am. J. Bot. 91 (2004), 1656–1665.
173. [173] Gensel, P.G., The earliest land plants. Annu. Rev. Ecol. Evol. Syst. 39 (2008), 459–477.
174. [174] Hu, L., Liu, S., Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers. Genet. Mol. Biol. 34 (2011), 624–633.
175. [175] Pereira-Santana, A., Alcaraz, L.D., Castaño, E., Sanchez-Calderon, L., Sanchez-Teyer, F., Rodriguez-Zapata, L., Comparative genomics of NAC transcriptional factors in angiosperms: implications for the adaptation and diversification of flowering plants. PLoS One, 10, 2015, e0141866.
176. [176] Blanc, G., Hokamp, K., Wolfe, K.H., A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13 (2003), 137–144.
177. [177] 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.
178. [178] Zhang, J., Jianzhi, Z., Evolution by gene duplication: an update. Trends Ecol. Evol. 18 (2003), 292–298.
179. [179] Jiang, N., Bao, Z., Zhang, X., Eddy, S.R., Wessler, S.R., Pack-MULE transposable elements mediate gene evolution in plants. Nature 431 (2004), 569–573.
180. [180] Drouin, G., Dover, G.A., Independent gene evolution in the potato actin gene family demonstrated by phylogenetic procedures for resolving gene conversions and the phylogeny of angiosperm actin genes. J. Mol. Evol. 31 (1990), 132–150.
181. [181] Brosius, J., Retroposons—seeds of evolution. Science, 251, 1991, 753.
182. [182] Yu, J., Ke, T., Tehrim, S., Sun, F., Liao, B., Hua, W., PTGBase: an integrated database to study tandem duplicated genes in plants. Database, 2015, 2015, 10.1093/database/bav017.
183. [183] 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.
184. [184] 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. U. S. A. 102 (2005), 5454–5459.
185. [185] Hanada, K., Zou, C., Lehti-Shiu, M.D., Shinozaki, K., Shiu, S.-H., Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148 (2008), 993–1003.
186. [186] Li, X., Duan, X., Jiang, H., Sun, Y., Tang, Y., Yuan, Z., Guo, J., Liang, W., Chen, L., Yin, J., Ma, H., Wang, J., Zhang, D., Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol. 141 (2006), 1167–1184.
187. [187] Wilkins, O., Nahal, H., Foong, J., Provart, N.J., Campbell, M.M., Expansion and diversification of the Populus R2R3-MYB family of transcription factors. Plant Physiol. 149 (2009), 981–993.
188. [188] Jiang, N., Ferguson, A.A., Slotkin, R.K., Lisch, D., Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition. Proc. Natl. Acad. Sci. U. S. A. 108 (2011), 1537–1542.
189. [189] Du, C., Fefelova, N., Caronna, J., He, L., Dooner, H.K., The polychromatic Helitron landscape of the maize genome. Proc. Natl. Acad. Sci. U. S. A. 106 (2009), 19916–19921.
190. [190] Li, Z., Defoort, J., Tasdighian, S., Maere, S., Van de Peer, Y., De Smet, R., Gene duplicability of core genes is highly consistent across all angiosperms. Plant Cell 28 (2016), 326–344.
191. [191] Guo, X., Zhang, Z., Gerstein, M.B., Zheng, D., Small RNAs originated from pseudogenes: cis- or trans-acting?. PLoS Comput. Biol., 5, 2009, e1000449.
192. [192] Zou, C., Lehti-Shiu, M.D., Thibaud-Nissen, F., Prakash, T., Buell, C.R., Shiu, S.-H., Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. Plant Physiol. 151 (2009), 3–15.
193. [193] Nam, J., Kim, J., Lee, S., An, G., Ma, H., Nei, M., Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc. Natl. Acad. Sci. U. S. A. 101 (2004), 1910–1915.
194. [194] Moghe, G.D., Hufnagel, D.E., Tang, H., Xiao, Y., Dworkin, I., Town, C.D., Conner, J.K., Shiu, S.-H., 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 (2014), 1925–1937.
195. [195] McAdams, H.H., Arkin, A., It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 15 (1999), 65–69.
196. [196] Kitano, H., Biological robustness. Nat. Rev. Genet. 5 (2004), 826–837.
197. [197] Zhou, Z.F., Xiao, B.L., Zhang, G.Y., Zhuang, L.Z., A study of the effect of B-EP and naloxone on the function of the hypothalamo-pituitary-testicular axis of the rat. J. Androl. 11 (1990), 233–239.
198. [198] de Martino, G., Pan, I., Emmanuel, E., Levy, A., Irish, V.F., Functional analyses of two tomato APETALA3 genes demonstrate diversification in their roles in regulating floral development. Plant Cell 18 (2006), 1833–1845.
199. [199] Hanada, K., Kuromori, T., Myouga, F., Toyoda, T., Li, W.-H., Shinozaki, K., Evolutionary persistence of functional compensation by duplicate genes in Arabidopsis. Genome Biol. Evol. 1 (2009), 409–414.
200. [200] Nowak, M.A., Boerlijst, M.C., Cooke, J., Smith, J.M., Evolution of genetic redundancy. Nature 388 (1997), 167–171.
201. [201] Ohno, S., Evolution by Gene Duplication. 1970, Springer.
202. [202] Rijpkema, A.S., Royaert, S., Zethof, J., van der Weerden, G., Gerats, T., Vandenbussche, M., Analysis of the Petunia TM6 MADS box gene reveals functional divergence within the DEF/AP3 lineage. Plant Cell 18 (2006), 1819–1832.
203. [203] Kramer, E.M., Holappa, L., Gould, B., Jaramillo, M.A., Setnikov, D., Santiago, P.M., Elaboration of B gene function to include the identity of novel floral organs in the lower eudicot Aquilegia. Plant Cell 19 (2007), 750–766.
204. [204] Rasmussen, D.A., Kramer, E.M., Zimmer, E.A., One size fits all? Molecular evidence for a commonly inherited petal identity program in Ranunculales. Am. J. Bot. 96 (2009), 96–109.
205. [205] Mondragón-Palomino, M., Theissen, G., Conserved differential expression of paralogous DEFICIENS- and GLOBOSA-like MADS-box genes in the flowers of Orchidaceae: refining the “orchid code”. Plant J. 66 (2011), 1008–1019.
206. [206] Furumizu, C., Alvarez, J.P., Sakakibara, K., Bowman, J.L., Antagonistic roles for KNOX1 and KNOX2 genes in patterning the land plant body plan following an ancient gene duplication. PLoS Genet., 11, 2015, e1004980.
207. [207] Liu, H., Liu, H., Zhou, L., Zhang, Z., Zhang, X., Wang, M., Li, H., Lin, Z., Parallel domestication of the heading date 1 gene in cereals. Mol. Biol. Evol. 32 (2015), 2726–2737.
208. [208] Hittinger, C.T., Carroll, S.B., Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449 (2007), 677–681.
209. [209] Des Marais, D.L., Rausher, M.D., Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454 (2008), 762–765.
210. [210] Huang, R., Hippauf, F., Rohrbeck, D., Haustein, M., Wenke, K., Feike, J., Sorrelle, N., Piechulla, B., Barkman, T.J., Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates. Proc. Natl. Acad. Sci. U. S. A. 109 (2012), 2966–2971.
211. [211] Sikosek, T., Chan, H.S., Bornberg-Bauer, E., Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness. Proc. Natl. Acad. Sci. U. S. A. 109 (2012), 14888–14893.
212. [212] Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., Postlethwait, J., Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151 (1999), 1531–1545.
213. [213] Birchler, J.A., Riddle, N.C., Auger, D.L., Veitia, R.A., Dosage balance in gene regulation: biological implications. Trends Genet. 21 (2005), 219–226.
214. [214] Freeling, M., Thomas, B.C., Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 16 (2006), 805–814.
215. [215] Birchler, J.A., Veitia, R.A., The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19 (2007), 395–402.
216. [216] Birchler, J.A., Veitia, R.A., The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol. 186 (2010), 54–62.
217. [217] Veitia, R.A., Exploring the etiology of haploinsufficiency. BioEssays 24 (2002), 175–184.
218. [218] Papp, B., Pál, C., Hurst, L.D., Dosage sensitivity and the evolution of gene families in yeast. Nature 424 (2003), 194–197.
219. [219] Schnable, J.C., Pedersen, B.S., Subramaniam, S., Freeling, M., Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses. Front. Plant Sci., 2, 2011, 2.
220. [220] Ganko, E.W., Meyers, B.C., Vision, T.J., Divergence in expression between duplicated genes in Arabidopsis. Mol. Biol. Evol. 24 (2007), 2298–2309.
221. [221] Renny-Byfield, S., Gallagher, J.P., Grover, C.E., Szadkowski, E., Page, J.T., Udall, J.A., Wang, X., Paterson, A.H., Wendel, J.F., Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol. Evol. 6 (2014), 559–571.
222. [222] Drea, S., Hileman, L.C., de Martino, G., Irish, V.F., Functional analyses of genetic pathways controlling petal specification in poppy. Development 134 (2007), 4157–4166.
223. [223] Sakuma, S., Pourkheirandish, M., Hensel, G., Kumlehn, J., Stein, N., Tagiri, A., Yamaji, N., Ma, J.F., Sassa, H., Koba, T., Komatsuda, T., Divergence of expression pattern contributed to neofunctionalization of duplicated HD-Zip I transcription factor in barley. New Phytol. 197 (2013), 939–948.
224. [224] Lehti-Shiu, M.D., Uygun, S., Moghe, G.D., Panchy, N., Fang, L., Hufnagel, D.E., Jasicki, H.L., Feig, M., Shiu, S.-H., Molecular evidence for functional divergence and decay of a transcription factor derived from whole-genome duplication in Arabidopsis thaliana. Plant Physiol. 168 (2015), 1717–1734.
225. [225] Haberer, G., Hindemitt, T., Meyers, B.C., Mayer, K.F.X., Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol. 136 (2004), 3009–3022.
226. [226] Ha, M., Kim, E.-D., Chen, Z.J., Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc. Natl. Acad. Sci. U. S. A. 106 (2009), 2295–2300.
227. [227] Hughes, A.L., Friedman, R., Expression patterns of duplicate genes in the developing root in Arabidopsis thaliana. J. Mol. Evol. 60 (2005), 247–256.
228. [228] Geuten, K., Viaene, T., Irish, V.F., Robustness and evolvability in the B-system of flower development. Ann. Bot. 107 (2011), 1545–1556.
229. [229] Vandenbussche, M., Zethof, J., Royaert, S., Weterings, K., Gerats, T., The duplicated B-class heterodimer model: whorl-specific effects and complex genetic interactions in Petunia hybrida flower development. Plant Cell 16 (2004), 741–754.
230. [230] McGonigle, B., Bouhidel, K., Irish, V.F., Nuclear localization of the Arabidopsis APETALA3 and PISTILLATA homeotic gene products depends on their simultaneous expression. Genes Dev. 10 (1996), 1812–1821.
231. [231] Irish, V.F., Evolution of petal identity. J. Exp. Bot. 60 (2009), 2517–2527.
232. [232] Lenser, T., Theissen, G., Dittrich, P., Developmental robustness by obligate interaction of class B floral homeotic genes and proteins. PLoS Comput. Biol., 5, 2009, e1000264.
233. [233] Liu, T.L., Newton, L., Liu, M.-J., Shiu, S.-H., Farré, E.M., A G-box-like motif is necessary for transcriptional regulation by circadian pseudo-response regulators in Arabidopsis. Plant Physiol. 170 (2016), 528–539.
234. [234] Weirauch, M.T., Yang, A., Albu, M., Cote, A.G., Montenegro-Montero, A., Drewe, P., Najafabadi, H.S., Lambert, S.A., Mann, I., Cook, K., Zheng, H., Goity, A., van Bakel, H., Lozano, J.-C., Galli, M., Lewsey, M.G., Huang, E., Mukherjee, T., Chen, X., Reece-Hoyes, J.S., Govindarajan, S., Shaulsky, G., Walhout, A.J.M., Bouget, F.-Y., Ratsch, G., Larrondo, L.F., Ecker, J.R., Hughes, T.R., Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158 (2014), 1431–1443.
235. [235] Arsovski, A.A., Pradinuk, J., Guo, X.Q., Wang, S., Adams, K.L., Evolution of Cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis. Plant Physiol. 169 (2015), 2982–2991.
236. [236] Rensing, S.A., Gene duplication as a driver of plant morphogenetic evolution. Curr. Opin. Plant Biol. 17 (2014), 43–48.
237. [237] Smaczniak, C., Immink, R.G.H., Angenent, G.C., Kaufmann, K., Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development 139 (2012), 3081–3098.
238. [238] Becker, A., Theissen, G., The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol. Phylogenet. Evol. 29 (2003), 464–489.
239. [239] Krizek, B.A., Fletcher, J.C., Molecular mechanisms of flower development: an armchair guide. Nat. Rev. Genet. 6 (2005), 688–698.
240. [240] Theissen, G., Melzer, R., Molecular mechanisms underlying origin and diversification of the angiosperm flower. Ann. Bot. 100 (2007), 603–619.
241. [241] Theissen, G., Development of floral organ identity: stories from the MADS house. Curr. Opin. Plant Biol. 4 (2001), 75–85.
242. [242] Theissen, G., Saedler, H., Plant biology. Floral quartets. Nature 409 (2001), 469–471.
243. [243] Melzer, R., Härter, A., Rümpler, F., Kim, S., Soltis, P.S., Soltis, D.E., Theißen, G., DEF- and GLO-like proteins may have lost most of their interaction partners during angiosperm evolution. Ann. Bot. 114 (2014), 1431–1443.
244. [244] Li, L., Yu, X.-X., Guo, C.-C., Duan, X.-S., Shan, H.-Y., Zhang, R., Xu, G.-X., Kong, H.-Z., Interactions among proteins of floral MADS-box genes in Nuphar pumila (Nymphaeaceae) and the most recent common ancestor of extant angiosperms help understand the underlying mechanisms of the origin of the flower: evolution of PPIs among floral MADS-box genes. J. Syst. Evol. 53 (2015), 285–296.
245. [245] Pires, N.D., Dolan, L., Morphological evolution in land plants: new designs with old genes. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 367 (2012), 508–518.
246. [246] True, J.R., Carroll, S.B., Gene co-option in physiological and morphological evolution. Annu. Rev. Cell Dev. Biol. 18 (2002), 53–80.
247. [247] Pires, N.D., Yi, K., Breuninger, H., Catarino, B., Menand, B., Dolan, L., Recruitment and remodeling of an ancient gene regulatory network during land plant evolution. Proc. Natl. Acad. Sci. U. S. A. 110 (2013), 9571–9576.
248. [248] Tam, T.H.Y., Catarino, B., Dolan, L., Conserved regulatory mechanism controls the development of cells with rooting functions in land plants. Proc. Natl. Acad. Sci. U. S. A. 112 (2015), E3959–E3968.
249. [249] Lotan, T., Ohto, M., Yee, K.M., West, M.A., Lo, R., Kwong, R.W., Yamagishi, K., Fischer, R.L., Goldberg, R.B., Harada, J.J., Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell 93 (1998), 1195–1205.
250. [250] Kirkbride, R.C., Fischer, R.L., Harada, J.J., LEAFY COTYLEDON1, a key regulator of seed development, is expressed in vegetative and sexual propagules of Selaginella moellendorffii. PLoS One, 8, 2013, e67971.
251. [251] Xie, Z., Li, X., Glover, B.J., Bai, S., Rao, G.-Y., Luo, J., Yang, J., Duplication and functional diversification of HAP3 genes leading to the origin of the seed-developmental regulatory gene, LEAFY COTYLEDON1 (LEC1), in nonseed plant genomes. Mol. Biol. Evol. 25 (2008), 1581–1592.
252. [252] Garcês, H.M.P., Champagne, C.E.M., Townsley, B.T., Park, S., Malhó, R., Pedroso, M.C., Harada, J.J., Sinha, N.R., Evolution of asexual reproduction in leaves of the genus Kalanchoë. Proc. Natl. Acad. Sci. U. S. A. 104 (2007), 15578–15583.
253. [253] Garcês, H.M.P., Koenig, D., Townsley, B.T., Kim, M., Sinha, N.R., Truncation of LEAFY COTYLEDON1 protein is required for asexual reproduction in Kalanchoë daigremontiana. Plant Physiol. 165 (2014), 196–206.
254. [254] Harrison, C.J., Corley, S.B., Moylan, E.C., Alexander, D.L., Scotland, R.W., Langdale, J.A., Independent recruitment of a conserved developmental mechanism during leaf evolution. Nature 434 (2005), 509–514.
255. [255] Tomescu, A.M.F., Megaphylls, microphylls and the evolution of leaf development. Trends Plant Sci. 14 (2009), 5–12.
256. [256] Lincoln, C., Long, J., Yamaguchi, J., Serikawa, K., Hake, S., A knotted1-like homeobox gene in Arabidopsis is expressed in the vegetative meristem and dramatically alters leaf morphology when overexpressed in transgenic plants. Plant Cell 6 (1994), 1859–1876.
257. [257] Sinha, N.R., Williams, R.E., Hake, S., Overexpression of the maize homeo box gene, KNOTTED-1, causes a switch from determinate to indeterminate cell fates. Genes Dev. 7 (1993), 787–795.
258. [258] Vollbrecht, E., Veit, B., Sinha, N., Hake, S., The developmental gene Knotted-1 is a member of a maize homeobox gene family. Nature 350 (1991), 241–243.
259. [259] Byrne, M.E., Barley, R., Curtis, M., Arroyo, J.M., Dunham, M., Hudson, A., Martienssen, R.A., Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature 408 (2000), 967–971.
260. [260] Ori, N., Eshed, Y., Chuck, G., Bowman, J.L., Hake, S., Mechanisms that control knox gene expression in the Arabidopsis shoot. Development 127 (2000), 5523–5532.
261. [261] Tsiantis, M., Schneeberger, R., Golz, J.F., Freeling, M., Langdale, J.A., The maize rough sheath2 gene and leaf development programs in monocot and dicot plants. Science 284 (1999), 154–156.
262. [262] Timmermans, M.C., Hudson, A., Becraft, P.W., Nelson, T., ROUGH SHEATH2: a Myb protein that represses knox homeobox genes in maize lateral organ primordia. Science 284 (1999), 151–153.
263. [263] Waites, R., Selvadurai, H.R., Oliver, I.R., Hudson, A., The PHANTASTICA gene encodes a MYB transcription factor involved in growth and dorsoventrality of lateral organs in Antirrhinum. Cell 93 (1998), 779–789.
264. [264] Pozzi, C., Rossini, L., Agosti, F., Patterns and symmetries in leaf development. Semin. Cell Dev. Biol. 12 (2001), 363–372.
265. [265] Phelps-Durr, T.L., Thomas, J., Vahab, P., Timmermans, M.C.P., Maize rough sheath2 and its Arabidopsis orthologue ASYMMETRIC LEAVES1 interact with HIRA, a predicted histone chaperone, to maintain knox gene silencing and determinacy during organogenesis. Plant Cell 17 (2005), 2886–2898.
266. [266] Zhang, W., Kramer, E.M., Davis, C.C., Floral symmetry genes and the origin and maintenance of zygomorphy in a plant-pollinator mutualism. Proc. Natl. Acad. Sci. U. S. A. 107 (2010), 6388–6393.
267. [267] Sargent, R.D., Floral symmetry affects speciation rates in angiosperms. Proc. Biol. Sci. 271 (2004), 603–608.
268. [268] Corley, S.B., Carpenter, R., Copsey, L., Coen, E., Floral asymmetry involves an interplay between TCP and MYB transcription factors in Antirrhinum. Proc. Natl. Acad. Sci. U. S. A. 102 (2005), 5068–5073.
269. [269] Feng, X., Zhao, Z., Tian, Z., Xu, S., Luo, Y., Cai, Z., Wang, Y., Yang, J., Wang, Z., Weng, L., Chen, J., Zheng, L., Guo, X., Luo, J., Sato, S., Tabata, S., Ma, W., Cao, X., Hu, X., Sun, C., Luo, D., Control of petal shape and floral zygomorphy in Lotus japonicus. Proc. Natl. Acad. Sci. U. S. A. 103 (2006), 4970–4975.
270. [270] Wang, Z., Luo, Y., Li, X., Wang, L., Xu, S., Yang, J., Weng, L., Sato, S., Tabata, S., Ambrose, M., Rameau, C., Feng, X., Hu, X., Luo, D., Genetic control of floral zygomorphy in pea (Pisum sativum L.). Proc. Natl. Acad. Sci. U. S. A. 105 (2008), 10414–10419.
271. [271] Citerne, H.L., Pennington, R.T., Cronk, Q.C.B., An apparent reversal in floral symmetry in the legume Cadia is a homeotic transformation. Proc. Natl. Acad. Sci. U. S. A. 103 (2006), 12017–12020.
272. [272] Yang, X., Pang, H.-B., Liu, B.-L., Qiu, Z.-J., Gao, Q., Wei, L., Dong, Y., Wang, Y.-Z., Evolution of double positive autoregulatory feedback loops in CYCLOIDEA2 clade genes is associated with the origin of floral zygomorphy. Plant Cell 24 (2012), 1834–1847.
273. [273] Hileman, L.C., Trends in flower symmetry evolution revealed through phylogenetic and developmental genetic advances. Philos. Trans. R. Soc. Lond. B Biol. Sci., 369, 2014, 10.1098/rstb.2013.0348.
274. [274] Cubas, P., Floral zygomorphy, the recurring evolution of a successful trait. BioEssays 26 (2004), 1175–1184.
275. [275] Hay, A., Tsiantis, M., The genetic basis for differences in leaf form between Arabidopsis thaliana and its wild relative Cardamine hirsuta. Nat. Genet. 38 (2006), 942–947.
276. [276] Shani, E., Burko, Y., Ben-Yaakov, L., Berger, Y., Amsellem, Z., Goldshmidt, A., Sharon, E., Ori, N., Stage-specific regulation of Solanum lycopersicum leaf maturation by class 1 KNOTTED1-LIKE HOMEOBOX proteins. Plant Cell 21 (2009), 3078–3092.
277. [277] Peng, J., Yu, J., Wang, H., Guo, Y., Li, G., Bai, G., Chen, R., Regulation of compound leaf development in Medicago truncatula by fused compound leaf1, a class M KNOX gene. Plant Cell 23 (2011), 3929–3943.
278. [278] Sakakibara, K., Nishiyama, T., Deguchi, H., Hasebe, M., Class 1 KNOX genes are not involved in shoot development in the moss Physcomitrella patens but do function in sporophyte development. Evol. Dev. 10 (2008), 555–566.
279. [279] Sano, R., Juárez, C.M., Hass, B., Sakakibara, K., Ito, M., Banks, J.A., Hasebe, M., KNOX homeobox genes potentially have similar function in both diploid unicellular and multicellular meristems, but not in haploid meristems. Evol. Dev. 7 (2005), 69–78.
280. [280] Dardick, C., Callahan, A.M., Evolution of the fruit endocarp: molecular mechanisms underlying adaptations in seed protection and dispersal strategies. Front. Plant Sci., 5, 2014, 284.
281. [281] Fourquin, C., del Cerro, C., Victoria, F.C., Vialette-Guiraud, A., de Oliveira, A.C., Ferrándiz, C., A change in SHATTERPROOF protein lies at the origin of a fruit morphological novelty and a new strategy for seed dispersal in medicago genus. Plant Physiol. 162 (2013), 907–917.
282. [282] Gu, Q., Ferrándiz, C., Yanofsky, M.F., Martienssen, R., The FRUITFULL MADS-box gene mediates cell differentiation during Arabidopsis fruit development. Development 125 (1998), 1509–1517.
283. [283] Litt, A., Irish, V.F., Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development. Genetics 165 (2003), 821–833.
284. [284] Pabón-Mora, N., Sharma, B., Holappa, L.D., Kramer, E.M., Litt, A., The Aquilegia FRUITFULL-like genes play key roles in leaf morphogenesis and inflorescence development. Plant J. 74 (2013), 197–212.
285. [285] McCarthy, E.W., Mohamed, A., Litt, A., Functional divergence of APETALA1 and FRUITFULL is due to changes in both regulation and coding sequence. Front. Plant Sci., 6, 2015, 1076.
286. [286] Liu, Y., Zhang, D., Ping, J., Li, S., Chen, Z., Ma, J., Innovation of a regulatory mechanism modulating semi-determinate stem growth through artificial selection in soybean. PLoS Genet., 12, 2016, e1005818.
287. [287] Weirauch, M.T., Hughes, T.R., A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. Subcell. Biochem. 52 (2011), 25–73.
288. [288] Weng, J.-K., Chapple, C., The origin and evolution of lignin biosynthesis. New Phytol. 187 (2010), 273–285.
289. [289] Nakano, Y., Yamaguchi, M., Endo, H., Rejab, N.A., Ohtani, M., NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants. Front. Plant Sci., 6, 2015, 288.
290. [290] Xu, B., Ohtani, M., Yamaguchi, M., Toyooka, K., Wakazaki, M., Sato, M., Kubo, M., Nakano, Y., Sano, R., Hiwatashi, Y., Murata, T., Kurata, T., Yoneda, A., Kato, K., Hasebe, M., Demura, T., Contribution of NAC transcription factors to plant adaptation to land. Science 343 (2014), 1505–1508.
291. [291] Schmid, K.M., Ohlrogge, J.B., Chapter 4 Lipid metabolism in plants. Biochemistry of Lipids, Lipoproteins and Membranes, fourth ed., 2002, Elsevier, 93–126.
292. [292] Wang, H.-W., Zhang, B., Hao, Y.-J., Huang, J., Tian, A.-G., Liao, Y., Zhang, J.-S., Chen, S.-Y., The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. Plant J. 52 (2007), 716–729.
293. [293] Cernac, A., Benning, C., WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis. Plant J. 40 (2004), 575–585.
294. [294] Liu, J., Hua, W., Zhan, G., Wei, F., Wang, X., Liu, G., Wang, H., Increasing seed mass and oil content in transgenic Arabidopsis by the overexpression of wri1-like gene from Brassica napus. Plant Physiol. Biochem. 48 (2010), 9–15.
295. [295] Pouvreau, B., Baud, S., Vernoud, V., Morin, V., Py, C., Gendrot, G., Pichon, J.-P., Rouster, J., Paul, W., Rogowsky, P.M., Duplicate maize Wrinkled1 transcription factors activate target genes involved in seed oil biosynthesis. Plant Physiol. 156 (2011), 674–686.
296. [296] Shen, B., Allen, W.B., Zheng, P., Li, C., Glassman, K., Ranch, J., Nubel, D., Tarczynski, M.C., Expression of ZmLEC1 and ZmWRI1 increases seed oil production in maize. Plant Physiol. 153 (2010), 980–987.
297. [297] Ma, W., Kong, Q., Arondel, V., Kilaru, A., Bates, P.D., Thrower, N.A., Benning, C., Ohlrogge, J.B., Wrinkled1, a ubiquitous regulator in oil accumulating tissues from Arabidopsis embryos to oil palm mesocarp. PLoS One, 8, 2013, e68887.
298. [298] A. To, Joubès, J., Barthole, G., Lécureuil, A., Scagnelli, A., Jasinski, S., Lepiniec, L., Baud, S., WRINKLED transcription factors orchestrate tissue-specific regulation of fatty acid biosynthesis in Arabidopsis. Plant Cell 24 (2012), 5007–5023.
299. [299] Kilaru, A., Cao, X., Dabbs, P.B., Sung, H.-J., Rahman, M.M., Thrower, N., Zynda, G., Podicheti, R., Ibarra-Laclette, E., Herrera-Estrella, L., Mockaitis, K., Ohlrogge, J.B., Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp. BMC Plant Biol., 15, 2015, 203.
300. [300] Pichersky, E., Lewinsohn, E., Convergent evolution in plant specialized metabolism. Annu. Rev. Plant Biol. 62 (2011), 549–566.
301. [301] Grubb, C.D., Abel, S., Glucosinolate metabolism and its control. Trends Plant Sci. 11 (2006), 89–100.
302. [302] Bekaert, M., Edger, P.P., Hudson, C.M., Pires, J.C., Conant, G.C., Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis. New Phytol. 196 (2012), 596–605.
303. [303] Edger, P.P., Heidel-Fischer, H.M., Bekaert, M., Rota, J., Glöckner, G., Platts, A.E., Heckel, D.G., Der, J.P., Wafula, E.K., Tang, M., Hofberger, J.A., Smithson, A., Hall, J.C., Blanchette, M., Bureau, T.E., Wright, S.I., dePamphilis, C.W., Schranz, M.E., Barker, M.S., Conant, G.C., Wahlberg, N., Vogel, H., Pires, J.C., Wheat, C.W., The butterfly plant arms-race escalated by gene and genome duplications. Proc. Natl. Acad. Sci. U. S. A. 112 (2015), 8362–8366.
304. [304] Frerigmann, H., Gigolashvili, T., MYB34, MYB51, and MYB122 distinctly regulate indolic glucosinolate biosynthesis in Arabidopsis thaliana. Mol. Plant 7 (2014), 814–828.
305. [305] Sønderby, I.E., Burow, M., Rowe, H.C., Kliebenstein, D.J., Halkier, B.A., A complex interplay of three R2R3 MYB transcription factors determines the profile of aliphatic glucosinolates in Arabidopsis. Plant Physiol. 153 (2010), 348–363.
306. [306] Hirai, M.Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R., Sakurai, N., Suzuki, H., Aoki, K., Goda, H., Nishizawa, O.I., Shibata, D., Saito, K., Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc. Natl. Acad. Sci. U. S. A. 104 (2007), 6478–6483.
307. [307] Celenza, J.L., Quiel, J.A., Smolen, G.A., Merrikh, H., Silvestro, A.R., Normanly, J., Bender, J., The Arabidopsis ATR1 Myb transcription factor controls indolic glucosinolate homeostasis. Plant Physiol. 137 (2005), 253–262.
308. [308] Zhang, Y., Li, B., Huai, D., Zhou, Y., Kliebenstein, D.J., The conserved transcription factors, MYB115 and MYB118, control expression of the newly evolved benzoyloxy glucosinolate pathway in Arabidopsis thaliana. Front. Plant Sci., 6, 2015, 343.
309. [309] Michaels, S.D., Amasino, R.M., FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11 (1999), 949–956.
310. [310] Ruelens, P., de Maagd, R.A., Proost, S., Theißen, G., Geuten, K., Kaufmann, K., FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes. Nat. Commun., 4, 2013, 2280.
311. [311] Shindo, C., Aranzana, M.J., Lister, C., Baxter, C., Nicholls, C., Nordborg, M., Dean, C., Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis. Plant Physiol. 138 (2005), 1163–1173.
312. [312] Caicedo, A.L., Stinchcombe, J.R., Olsen, K.M., Schmitt, J., Purugganan, M.D., Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait. Proc. Natl. Acad. Sci. U. S. A. 101 (2004), 15670–15675.
313. [313] Chiang, G.C.K., Barua, D., Kramer, E.M., Amasino, R.M., Donohue, K., Major flowering time gene, flowering locus C, regulates seed germination in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 106 (2009), 11661–11666.
314. [314] Putterill, J., Robson, F., Lee, K., Simon, R., Coupland, G., The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80 (1995), 847–857.
315. [315] Rosas, U., Mei, Y., Xie, Q., Banta, J.A., Zhou, R.W., Seufferheld, G., Gerard, S., Chou, L., Bhambhra, N., Parks, J.D., Flowers, J.M., McClung, C.R., Hanzawa, Y., Purugganan, M.D., Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS. Nat. Commun., 5, 2014, 3651.
316. [316] Simon, S., Rühl, M., de Montaigu, A., Wötzel, S., Coupland, G., Evolution of CONSTANS regulation and function after gene duplication produced a photoperiodic flowering switch in the Brassicaceae. Mol. Biol. Evol. 32 (2015), 2284–2301.
317. [317] Dietz, K.-J., Vogel, M.O., Viehhauser, A., AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling. Protoplasma 245 (2010), 3–14.
318. [318] Dey, S., Corina Vlot, A., Ethylene responsive factors in the orchestration of stress responses in monocotyledonous plants. Front. Plant Sci., 6, 2015, 640.
319. [319] Gutterson, N., Reuber, T.L., Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr. Opin. Plant Biol. 7 (2004), 465–471.
320. [320] Sun, S., Yu, J.-P., Chen, F., Zhao, T.-J., Fang, X.-H., Li, Y.-Q., Sui, S.-F., TINY, a dehydration-responsive element (DRE)-binding protein-like transcription factor connecting the DRE- and ethylene-responsive element-mediated signaling pathways in Arabidopsis. J. Biol. Chem. 283 (2008), 6261–6271.
321. [321] Nakano, T., Suzuki, K., Fujimura, T., Shinshi, H., Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 140 (2006), 411–432.
322. [322] Fukao, T., Bailey-Serres, J., Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proc. Natl. Acad. Sci. U. S. A. 105 (2008), 16814–16819.
323. [323] Xu, K., Xu, X., Fukao, T., Canlas, P., Maghirang-Rodriguez, R., Heuer, S., Ismail, A.M., Bailey-Serres, J., Ronald, P.C., Mackill, D.J., Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442 (2006), 705–708.
324. [324] Thomashow, M.F., Molecular basis of plant cold acclimation: insights gained from studying the CBF cold response pathway. Plant Physiol. 154 (2010), 571–577.
325. [325] Alonso-Blanco, C., Gomez-Mena, C., Llorente, F., Koornneef, M., Salinas, J., Martínez-Zapater, J.M., Genetic and molecular analyses of natural variation indicate CBF2 as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis. Plant Physiol. 139 (2005), 1304–1312.
326. [326] Ågrena, J., Oakley, C.G., McKay, J.K., Lovell, J.T., Schemske, D.W., Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 110 (2013), 21077–21082.
327. [327] Oakley, C.G., Ågren, J., Atchison, R.A., Schemske, D.W., QTL mapping of freezing tolerance: links to fitness and adaptive trade-offs. Mol. Ecol. 23 (2014), 4304–4315.
328. [328] Gehan, M.A., Park, S., Gilmour, S.J., An, C., Lee, C.-M., Thomashow, M.F., Natural variation in the C-repeat binding factor cold response pathway correlates with local adaptation of Arabidopsis ecotypes. Plant J. 84 (2015), 682–693.
329. [329] Sieber, A.-N., Longin, C.F.H., Leiser, W.L., Würschum, T., Copy Number Variation of CBF-A14 at the Fr-A2 Locus Determines Frost Tolerance in Winter Durum Wheat. 2016, Theor. Appl, Genet, 10.1007/s00122-016-2685-3.
330. [330] Francia, E., Barabaschi, D., Tondelli, A., Laidò, G., Rizza, F., Stanca, A.M., Busconi, M., Fogher, C., Stockinger, E.J., Pecchioni, N., Fine mapping of a HvCBF gene cluster at the frost resistance locus Fr-H2 in barley. Theor. Appl. Genet. 115 (2007), 1083–1091.
331. [331] Olsen, K.M., Wendel, J.F., Crop plants as models for understanding plant adaptation and diversification. Front. Plant Sci., 4, 2013, 290.
332. [332] Doebley, J., Plant science. Unfallen grains: how ancient farmers turned weeds into crops. Science 312 (2006), 1318–1319.
333. [333] Lenser, T., Theißen, G., Molecular mechanisms involved in convergent crop domestication. Trends Plant Sci. 18 (2013), 704–714.
334. [334] Doebley, J., Stec, A., Hubbard, L., The evolution of apical dominance in maize. Nature 386 (1997), 485–488.
335. [335] Studer, A., Zhao, Q., Ross-Ibarra, J., Doebley, J., Identification of a functional transposon insertion in the maize domestication gene tb1. Nat. Genet. 43 (2011), 1160–1163.
336. [336] Remigereau, M.-S., Lakis, G., Rekima, S., Leveugle, M., Fontaine, M.C., Langin, T., Sarr, A., Robert, T., Cereal domestication and evolution of branching: evidence for soft selection in the Tb1 orthologue of pearl millet (Pennisetum glaucum [L.] R. Br.). PLoS One, 6, 2011, e22404.
337. [337] Wang, H., Studer, A.J., Zhao, Q., Meeley, R., Doebley, J.F., Evidence that the origin of naked kernels during maize domestication was caused by a single amino acid substitution in tga1. Genetics 200 (2015), 965–974.
338. [338] Dorweiler, J., Stec, A., Kermicle, J., Doebley, J., Teosinte glume architecture 1: a genetic locus controlling a key step in maize evolution. Science 262 (1993), 233–235.
339. [339] Dorweiler, J., Doebley, J., Developmental analysis of teosinte glume architecture1: a key locus in the evolution of maize (Poaceae). Am. J. Bot., 84, 1997, 1313.
340. [340] Li, C., Zhou, A., Sang, T., Rice domestication by reducing shattering. Science 311 (2006), 1936–1939.
341. [341] Konishi, S., Izawa, T., Lin, S.Y., Ebana, K., Fukuta, Y., Sasaki, T., Yano, M., An SNP caused loss of seed shattering during rice domestication. Science 312 (2006), 1392–1396.
342. [342] Cannon, J.T., Vellutini, B.C., Smith, J. 3rd, Ronquist, F., Jondelius, U., Hejnol, A., Xenacoelomorpha is the sister group to Nephrozoa. Nature 530 (2016), 89–93.
343. [343] Ebersberger, I., de Matos Simoes, R., Kupczok, A., Gube, M., Kothe, E., Voigt, K., von Haeseler, A., A consistent phylogenetic backbone for the fungi. Mol. Biol. Evol. 29 (2012), 1319–1334.
344. [344] Brown, J.W., Sorhannus, U., A molecular genetic timescale for the diversification of autotrophic stramenopiles (Ochrophyta): substantive underestimation of putative fossil ages. PLoS One, 5, 2010, 10.1371/journal.pone.0012759.
345. [345] Kuvardina, O.N., Leander, B.S., Aleshin, V.V., Myl'nikov, A.P., Keeling, P.J., Simdyanov, T.G., The phylogeny of colpodellids (Alveolata) using small subunit rRNA gene sequences suggests they are the free-living sister group to apicomplexans. J. Eukaryot. Microbiol. 49 (2002), 498–504.
346. [346] Finn, R.D., Clements, J., Eddy, S.R., HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39 (2011), W29–W37.
347. [347] Wu, G., Hufnagel, D.E., Denton, A.K., Shiu, S.-H., Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains. BMC Genomics, 16, 2015, 149.
348. [348] Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N., Rokhsar, D.S., Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40 (2012), D1178–D1186.
349. [349] Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D., Freeling, M., Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol. 148 (2008), 1772–1781.
350. [350] Lyons, E., Freeling, M., How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 53 (2008), 661–673.