Transcription factors in rice: A genome-wide comparative analysis between monocots and eudicots

Plant Molecular Biology

Volumn 59, Issue 1, 2005, Pages 191-203

  Xiong, Yuqing ^a   Liu, Tieyan ^a   Tian, Chaoguang ^a   Sun, Shouhong ^a   Li, Jiayang ^a   Chen, Mingsheng ^a  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

Author keywords

Comparative genomics; Genome duplication; Transcription factor

Indexed keywords

GENES;

COMPARATIVE GENOMICS; GENOME DUPLICATION; TRANSCRIPTION FACTORS (TF);

CROPS;

ARABIDOPSIS PROTEIN; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ARABIDOPSIS; ARTICLE; CHROMOSOME MAP; COMPARATIVE STUDY; GENE DUPLICATION; GENETICS; GENOME; NUCLEIC ACID DATABASE; PHYLOGENY; PLANT CHROMOSOME; RICE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DATABASES, NUCLEIC ACID; GENE DUPLICATION; GENOME, PLANT; ORYZA SATIVA; PHYLOGENY; PLANT PROTEINS; TRANSCRIPTION FACTORS;

GENES; RICE;

ARABIDOPSIS; ARABIDOPSIS THALIANA; LILIOPSIDA; MAGNOLIOPHYTA; ORYZA SATIVA;

EID: 26444578198     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-005-6503-6     Document Type: Article

References (68)

1. B.A. Ambrose D.R. Lerner P. Ciceri C.M. Padilla M.F. Yanofsky R.J. Schmidt 2000 Molecular and genetic analyses of the silky1 gene reveal conservation in floral organ specification between eudicots and monocots Mol. Cell 5 569 579
2. A. Bateman E. Birney R. Durbin S.R. Eddy K.L. Howe E.L. Sonnhammer 2000 The Pfam protein families database Nucleic Acids Res 28 263 266
3. A. Becker G. Theissen 2003 The major clades of MADS-box genes and their role in the development and evolution of flowering plants Mol. Phylogenet. Evol. 29 464 489
4. P.N. Benfey D. Weigel 2001 Transcriptional networks controlling plant development Plant Physiol. 125 109 111
5. G. Blanc K. Hokamp K.H. Wolfe 2003 A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome Genome Res. 13 137 144
6. J.L. Bowman 2000 Axial patterning in leaves and other lateral organs Curr. Opin. Genet. Dev. 10 399 404
7. J.L. Bowman Y. Eshed S.F. Baum 2002 Establishment of polarity in angiosperm lateral organs Trends Genet. 18 134 141
8. J.L. Bowman D.R. Smyth 1999 CRABS CLAW, a gene that regulates carpel and nectary development in Arabidopsis, encodes a novel protein with zinc finger and helix-loop-helix domains Development 126 2387 2396
9. Q. Chen A. Atkinson D. Otsuga T. Christensen L. Reynolds G.N. Drews 1999 The Arabidopsis FILAMENTOUS FLOWER gene is required for flower formation Development 126 2715 2726
10. R. Chenna H. Sugawara T. Koike R. Lopez T.J. Gibson D.G. Higgins J.D. Thompson 2003 Multiple sequence alignment with the Clustal series of programs Nucleic Acids Res. 31 3497 3500
11. J. Doebley A. Stec L. Hubbard 1997 The evolution of apical dominance in maize Nature 386 485 488
12. Felsenstein, J. 1989. PHYLIP: phylogeny inference package. Cladistics S, pp. 164-166
13. Q. Feng Y. Zhang P. Hao S. Wang G. Fu Y. Huang Y. Li J. Zhu Y. Liu X. Hu P. Jia Q. Zhao K. Ying S. Yu Y. Tang Q. Weng L. Zhang Y. Lu J. Mu L.S. Zhang Z. Yu D. Fan X. Liu T. Lu C. Li Y. Wu T. Sun H. Lei T. Li H. Hu J. Guan M. Wu R. Zhang B. Zhou Z. Chen L. Chen Z. Jin R. Wang H. Yin Z. Cai S. Ren G. Lv W. Gu G. Zhu Y. Tu J. Jia J. Chen H. Kang X. Chen C. Shao Y. Sun Q. Hu X. Zhang W. Zhang L. Wang C. Ding H. Sheng J. Gu S. Chen L. Ni F. Zhu W. Chen L. Lan Y. Lai Z. Cheng M. Gu J. Jiang J. Li G. Hong Y. Xue B. Han 2002 Sequence and analysis of rice chromosome 4 Nature 420 316 320
14. N. Galtier M. Gouy C. Gautier 1996 SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny Comput. Appl. Biosci. 12 543 548
15. S.A. Goff D. Ricke T.H. Lan G. Presting R. Wang M. Dunn J. Glazebrook A. Sessions P. Oeller H. Varma D. Hadley D. Hutchison C. Martin F. Katagiri B.M. Lange T. Moughamer Y. Xia P. Budworth J. Zhong T. Miguel U. Paszkowski S. Zhang M. Colbert W.L. Sun L. Chen B. Cooper S. Park T.C. Wood L. Mao P. Quail R. Wing R. Dean Y. Yu A. Zharkikh R. Shen S. Sahasrabudhe A. Thomas R. Cannings A. Gutin D. Pruss J. Reid S. Tavtigian J. Mitchell G. Eldredge T. Scholl R.M. Miller S. Bhatnagar N. Adey T. Rubano N. Tusneem R. Robinson J. Feldhaus T. Macalma A. Oliphant S. Briggs 2002 A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science 296 92 100
16. T. Greb O. Clarenz E. Schafer D. Muller R. Herrero G. Schmitz K. Theres 2003 Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation Genes Dev. 17 1175 1187
17. S. Griffiths R.P. Dunford G. Coupland D.A. Laurie 2003 The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis Plant Physiol. 131 1855 1867
18. M.G. Heisler A. Atkinson Y.H. Bylstra R. Walsh D.R. Smyth 2001 SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein Development 128 1089 1098
19. A. Ikeda M. Ueguchi-Tanaka Y. Sonoda H. Kitano M. Koshioka Y. Futsuhara M. Matsuoka J. Yamaguchi 2001 Slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8 Plant Cell 13 999 1010
20. In-depth view of structure, activity, and evolution of rice chromosome 10. 2003. Science 300: 1566-1569
21. D.H. Jeong S. An H.G. Kang S. Moon J.J. Han S. Park H.S. Lee K. An G. An 2002 T-DNA insertional mutagenesis for activation tagging in rice Plant Physiol. 130 1636 1644
22. M.T. Juarez J.S. Kui J. Thomas B.A. Heller M.C. Timmermans 2004 MicroRNA-mediated repression of rolled leaf1 specifies maize leaf polarity Nature 428 84 88
23. R.A. Kerstetter K. Bollman R.A. Taylor K. Bomblies R.S. Poethig 2001 KANADI regulates organ polarity in Arabidopsis Nature 411 706 709
24. S. Kikuchi K. Satoh T. Nagata N. Kawagashira K. Doi N. Kishimoto J. Yazaki M. Ishikawa H. Yamada H. Ooka I. Hotta K. Kojima T. Namiki E. Ohneda W. Yahagi K. Suzuki C.J. Li K. Ohtsuki T. Shishiki Y. Otomo K. Murakami Y. Iida S. Sugano T. Fujimura Y. Suzuki Y. Tsunoda T. Kurosaki T. Kodama H. Masuda M. Kobayashi Q. Xie M. Lu R. Narikawa A. Sugiyama K. Mizuno S. Yokomizo J. Niikura R. Ikeda J. Ishibiki M. Kawamata A. Yoshimura J. Miura T. Kusumegi M. Oka R. Ryu M. Ueda K. Matsubara J. Kawai P. Carninci J. Adachi K. Aizawa T. Arakawa S. Fukuda A. Hara W. Hashizume N. Hayatsu K. Imotani Y. Ishii M. Itoh I. Kagawa S. Kondo H. Konno A. Miyazaki N. Osato Y. Ota R. Saito D. Sasaki K. Sato K. Shibata A. Shinagawa T. Shiraki M. Yoshino Y. Hayashizaki A. Yasunishi 2003 Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice Science 301 376 379
25. J.H. Kim D. Choi H. Kende 2003 The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis Plant J. 36 94 104
26. S. Kumar K. Tamura I.B. Jakobsen M. Nei 2001 MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 1244 1245
27. D. Leister 2004 Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene Trends Genet. 20 116 122
28. X. Li Q. Qian Z. Fu Y. Wang G. Xiong D. Zeng X. Wang X. Liu S. Teng F. Hiroshi M. Yuan D. Luo B. Han J. Li 2003 Control of tillering in rice Nature 422 618 621
29. Z. Li T.L. Thomas 1998 PEI1, an embryo-specific zinc finger protein gene required for heart-stage embryo formation in Arabidopsis Plant Cell 10 383 398
30. J.R. McConnell J. Emery Y. Eshed N. Bao J. Bowman M.K. Barton 2001 Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots Nature 411 709 713
31. W. McGinnis M.S. Levine E. Hafen A. Kuroiwa W.J. Gehring 1984 A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes Nature 308 428 433
32. M. Mena B.A. Ambrose R.B. Meeley S.P. Briggs M.F. Yanofsky R.J. Schmidt 1996 Diversification of C-function activity in maize flower development Science 274 1537 1540
33. A. Miyao K. Tanaka K. Murata H. Sawaki S. Takeda K. Abe Y. Shinozuka K. Onosato H. Hirochika 2003 Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome Plant Cell 15 1771 1780
34. M.A. Moreno L.C. Harper R.W. Krueger S.L. Dellaporta M. Freeling 1997 liguleless1 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis Genes Dev 11 616 628
35. N. Nagasawa M. Miyoshi Y. Sano H. Satoh H. Hirano H. Sakai Y. Nagato 2003 SUPERWOMAN1 and DROOPING LEAF genes control floral organ identity in rice Development 130 705 718
36. L. Parenicova S. de Folter M. Kieffer D.S. Horner C. Favalli J. Busscher H.E. Cook R.M. Ingram M.M. Kater B. Davies G.C. Angenent L. Colombo 2003 Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world Plant Cell 15 1538 1551
37. J. Peng D.E. Richards N.M. Hartley G.P. Murphy K.M. Devos J.E. Flintham J. Beales L.J. Fish A.J. Worland F. Pelica D. Sudhakar P. Christou J.W. Snape M.D. Gale N.P. Harberd 1999 'Green revolution' genes encode mutant gibberellin response modulators Nature 400 256 261
38. S. Rajani V. Sundaresan 2001 The Arabidopsis myc/bHLH gene ALCATRAZ enables cell separation in fruit dehiscence Curr. Biol. 11 1914 1922
39. J.L. Riechmann J. Heard G. Martin L. Reuber C. Jiang J. Keddie L. Adam O. Pineda O.J. Ratcliffe R.R. Samaha R. Creelman M. Pilgrim P. Broun J.Z. Zhang D. Ghandehari B.K. Sherman G. Yu 2000 Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes Science 290 2105 2110
40. J.L. Riechmann 2002 Meyerowitz CsaE Transcriptional regulation: a genomic overview Amerian Society of Plant Biologists Rockville
41. J.L. Riechmann E.M. Meyerowitz 1997 MADS domain proteins in plant development Biol. Chem. 378 1079 1101
42. A.A. Salamov V.V. Solovyev 2000 Ab initio gene finding in Drosophila genomic DNA Genome Res. 10 516 522
43. T. Sasaki T. Matsumoto K. Yamamoto K. Sakata T. Baba Y. Katayose J. Wu Y. Niimura Z. Cheng Y. Nagamura B.A. Antonio H. Kanamori S. Hosokawa M. Masukawa K. Arikawa Y. Chiden M. Hayashi M. Okamoto T. Ando H. Aoki K. Arita M. Hamada C. Harada S. Hijishita M. Honda Y. Ichikawa A. Idonuma M. Iijima M. Ikeda M. Ikeno S. Ito T. Ito Y. Ito A. Iwabuchi K. Kamiya W. Karasawa S. Katagiri A. Kikuta N. Kobayashi I. Kono K. Machita T. Maehara H. Mizuno T. Mizubayashi Y. Mukai H. Nagasaki M. Nakashima Y. Nakama Y. Nakamichi M. Nakamura N. Namiki M. Negishi I. Ohta N. Ono S. Saji K. Sakai M. Shibata T. Shimokawa A. Shomura J. Song Y. Takazaki K. Terasawa K. Tsuji K. Waki H. Yamagata H. Yamane S. Yoshiki R. Yoshihara K. Yukawa H. Zhong H. Iwama T. Endo H. Ito J.H. Hahn H.I. Kim M.Y. Eun M. Yano J. Jiang T. Gojobori 2002 The genome sequence and structure of rice chromosome 1 Nature 420 312 316
44. S. Sawa K. Watanabe K. Goto Y.G. Liu D. Shibata E. Kanaya E.H. Morita K. Okada 1999 FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains Genes Dev. 13 1079 1088
45. S. Schellmann A. Schnittger V. Kirik T. Wada K. Okada A. Beermann J. Thumfahrt G. Jurgens M. Hulskamp 2002 TRIPTYCHON and CAPRICE mediate lateral inhibition during trichome and root hair patterning in Arabidopsis Embo. J. 21 5036 5046
46. J. Schiefelbein 2003 Cell-fate specification in the epidermis: a common patterning mechanism in the root and shoot Curr. Opin. Plant Biol. 6 74 78
47. U. Schiefthaler S. Balasubramanian P. Sieber D. Chevalier E. Wisman K. Schneitz 1999 Molecular analysis of NOZZLE, a gene involved in pattern formation and early sporogenesis during sex organ development in Arabidopsis thaliana Proc. Natl. Acad. Sci. USA 96 11664 11669
48. K. Schumacher T. Schmitt M. Rossberg G. Schmitz K. Theres 1999 The lateral suppressor (Ls) gene of tomato encodes a new member of the VHIID protein family Proc. Natl. Acad. Sci. USA 96 290 295
49. M.P. Scott A.J. Weiner 1984 Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila Proc. Natl. Acad. Sci. USA 81 4115 4119
50. P.S. Soltis D.E. Soltis M.W. Chase 1999 Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology Nature 402 402 404
51. P.S. Soltis D.E. Soltis V. Savolainen P.R. Crane T.G. Barraclough 2002 Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils Proc. Natl. Acad. Sci. USA 99 4430 4435
52. M. Suzuki C.Y. Kao S. Cocciolone D.R. McCarty 2001 Maize VP1 complements Arabidopsis abi3 and confers a novel ABA/auxin interaction in roots Plant J. 28 409 418
53. H. Takatsuji 1998 Zinc-finger transcription factors in plants Cell Mol. Life Sci. 54 582 596
54. P.B. Talbert H.T. Adler D.W. Parks L. Comai 1995 The REVOLUTA gene is necessary for apical meristem development and for limiting cell divisions in the leaves and stems of Arabidopsis thaliana Development 121 2723 2735
55. G. Theissen A. Becker A. Di Rosa A. Kanno J.T. Kim T. Munster K.U. Winter H. Saedler 2000 A short history of MADS-box genes in plants Plant Mol. Biol. 42 115 149
56. G. Theodoris N. Inada M. Freeling 2003 Conservation and molecular dissection of ROUGH SHEATH2 and ASYMMETRIC LEAVES1 function in leaf development Proc. Natl. Acad. Sci. USA 100 6837 6842
57. C. Tian P. Wan S. Sun J. Li M. Chen 2004 Genome-wide analysis of the GRAS gene family in rice and Arabidopsis Plant Mol. Biol. 54 519 532
58. Tian, C., Xiong, Y., Liu, T., Sun, S., Chen., L. and Chen, M. 2005. Evidence for an ancient whole-genome duplication event in rice and other cereals. Acta Genetica Sinica (in press)
59. G. Toledo-Ortiz E. Huq P.H. Quail 2003 The Arabidopsis basic/helix-loop-helix transcription factor family Plant Cell 15 1749 1770
60. M. Vandenbussche J. Zethof S. Royaert K. Weterings T. Gerats 2004 The duplicated B-class heterodimer model: whorl-specific effects and complex genetic interactions in Petunia hybrida flower development Plant Cell 16 741 754
61. T. Wada T. Tachibana Y. Shimura K. Okada 1997 Epidermal cell differentiation in Arabidopsis determined by a Myb homolog, CPC Science 277 1113 1116
62. R.L. Wang A. Stec J. Hey L. Lukens J. Doebley 1999 The limits of selection during maize domestication Nature 398 236 239
63. N. Wikstrom V. Savolainen M.W. Chase 2001 Evolution of the angiosperms: calibrating the family tree Proc. R. Soc. Lond. B. Biol. Sci. 268 2211 2220
64. K.H. Wolfe M. Gouy Y.W. Yang P.M. Sharp W.H. Li 1989 Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data Proc. Natl. Acad. Sci. USA 86 6201 6205
65. T. Yamaguchi N. Nagasawa S. Kawasaki M. Matsuoka Y. Nagato H.Y. Hirano 2004 The YABBY gene DROOPING LEAF regulates carpel specification and midrib development in Oryza sativa Plant Cell 16 500 509
66. W.C. Yang D. Ye J. Xu V. Sundaresan 1999 The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein Genes Dev. 13 2108 2117
67. J. Yu S. Hu J. Wang G.K. Wong S. Li B. Liu Y. Deng L. Dai Y. Zhou X. Zhang M. Cao J. Liu J. Sun J. Tang Y. Chen X. Huang W. Lin C. Ye W. Tong L. Cong J. Geng Y. Han L. Li W. Li G. Hu J. Li Z. Liu Q. Qi T. Li X. Wang H. Lu T. Wu M. Zhu P. Ni H. Han W. Dong X. Ren X. Feng P. Cui X. Li H. Wang X. Xu W. Zhai Z. Xu J. Zhang S. He J. Xu K. Zhang X. Zheng J. Dong W. Zeng L. Tao J. Ye J. Tan X. Chen J. He D. Liu W. Tian C. Tian H. Xia Q. Bao G. Li H. Gao T. Cao W. Zhao P. Li W. Chen Y. Zhang J. Hu S. Liu J. Yang G. Zhang Y. Xiong Z. Li L. Mao C. Zhou Z. Zhu R. Chen B. Hao W. Zheng S. Chen W. Guo M. Tao L. Zhu L. Yuan H. Yang 2002 A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science 296 79 92
68. Q. Yuan S. Ouyang J. Liu B. Suh F. Cheung R. Sultana D. Lee J. Quackenbush C.R. Buell 2003 The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists Nucleic Acids Res. 31 229 233