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Transcription Factors in Rice: A Genome-wide Comparative Analysis between Monocots and Eudicots

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Abstract

It is not known how representative the Arabidopsis thaliana complement of transcription factors (TFs) is of other plants. The availability of rice (Oryza sativa) genome sequences makes possible a comparative analysis of TFs between monocots and eudicots, the two major monophyletic groups of angiosperms. Here, we identified 1611 TF genes that belong to 37 gene families in rice, comparable to the 1510 in Arabidopsis. Several gene subfamilies, but no families, were found to be lineage-specific. Phylogenetic analyses indicated that nearly half of the TF genes form clear orthologous pairs or groups, which were derived from 383 ancestral genes in the common ancestor of rice and Arabidopsis. Investigating gene duplication mechanisms revealed twelve pairs of large intragenomic duplicated blocks, which account for more than 40% of the rice genome. About 60% of the duplicated TF genes have been retained on duplicated segments. Functional conservation and diversification of TFs across monocot and eudicot lineages are discussed.

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References

  • B.A. Ambrose D.R. Lerner P. Ciceri C.M. Padilla M.F. Yanofsky R.J. Schmidt (2000) ArticleTitleMolecular and genetic analyses of the silky1 gene reveal conservation in floral organ specification between eudicots and monocots Mol. Cell 5 569–579 Occurrence Handle10882141 Occurrence Handle1:CAS:528:DC%2BD3cXisVWrs7k%3D Occurrence Handle10.1016/S1097-2765(00)80450-5

    Article  PubMed  CAS  Google Scholar 

  • A. Bateman E. Birney R. Durbin S.R. Eddy K.L. Howe E.L. Sonnhammer (2000) ArticleTitleThe Pfam protein families database Nucleic Acids Res 28 263–266 Occurrence Handle10592242 Occurrence Handle1:CAS:528:DC%2BD3cXhvVKjt7c%3D Occurrence Handle10.1093/nar/28.1.263

    Article  PubMed  CAS  Google Scholar 

  • A. Becker G. Theissen (2003) ArticleTitleThe major clades of MADS-box genes and their role in the development and evolution of flowering plants Mol. Phylogenet. Evol. 29 464–489 Occurrence Handle14615187 Occurrence Handle1:CAS:528:DC%2BD3sXovVWnur4%3D Occurrence Handle10.1016/S1055-7903(03)00207-0

    Article  PubMed  CAS  Google Scholar 

  • P.N. Benfey D. Weigel (2001) ArticleTitleTranscriptional networks controlling plant development Plant Physiol. 125 109–111 Occurrence Handle11154309 Occurrence Handle1:CAS:528:DC%2BD3MXjslymtb0%3D Occurrence Handle10.1104/pp.125.1.109

    Article  PubMed  CAS  Google Scholar 

  • G. Blanc K. Hokamp K.H. Wolfe (2003) ArticleTitleA recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome Genome Res. 13 137–144 Occurrence Handle12566392 Occurrence Handle1:CAS:528:DC%2BD3sXhtlCrs7o%3D Occurrence Handle10.1101/gr.751803

    Article  PubMed  CAS  Google Scholar 

  • J.L. Bowman (2000) ArticleTitleAxial patterning in leaves and other lateral organs Curr. Opin. Genet. Dev. 10 399–404 Occurrence Handle10889056 Occurrence Handle1:CAS:528:DC%2BD3cXlt1SjtbY%3D Occurrence Handle10.1016/S0959-437X(00)00103-9

    Article  PubMed  CAS  Google Scholar 

  • J.L. Bowman Y. Eshed S.F. Baum (2002) ArticleTitleEstablishment of polarity in angiosperm lateral organs Trends Genet. 18 134–141 Occurrence Handle11858837 Occurrence Handle1:CAS:528:DC%2BD38XhtlGju70%3D Occurrence Handle10.1016/S0168-9525(01)02601-4

    Article  PubMed  CAS  Google Scholar 

  • J.L. Bowman D.R. Smyth (1999) ArticleTitleCRABS 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 Occurrence Handle10225998 Occurrence Handle1:CAS:528:DyaK1MXktFWrtb8%3D

    PubMed  CAS  Google Scholar 

  • Q. Chen A. Atkinson D. Otsuga T. Christensen L. Reynolds G.N. Drews (1999) ArticleTitleThe Arabidopsis FILAMENTOUS FLOWER gene is required for flower formation Development 126 2715–2726 Occurrence Handle10331982 Occurrence Handle1:CAS:528:DyaK1MXks1Wqt70%3D

    PubMed  CAS  Google Scholar 

  • R. Chenna H. Sugawara T. Koike R. Lopez T.J. Gibson D.G. Higgins J.D. Thompson (2003) ArticleTitleMultiple sequence alignment with the Clustal series of programs Nucleic Acids Res. 31 3497–3500 Occurrence Handle12824352 Occurrence Handle1:CAS:528:DC%2BD3sXltVWjsrg%3D Occurrence Handle10.1093/nar/gkg500

    Article  PubMed  CAS  Google Scholar 

  • J. Doebley A. Stec L. Hubbard (1997) ArticleTitleThe evolution of apical dominance in maize Nature 386 485–488 Occurrence Handle9087405 Occurrence Handle1:CAS:528:DyaK2sXisVSqurc%3D Occurrence Handle10.1038/386485a0

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein, J. 1989. PHYLIP: phylogeny inference package. Cladistics S, pp. 164–166

  • 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) ArticleTitleSequence and analysis of rice chromosome 4 Nature 420 316–320 Occurrence Handle12447439 Occurrence Handle1:CAS:528:DC%2BD38XovVektL8%3D Occurrence Handle10.1038/nature01183

    Article  PubMed  CAS  Google Scholar 

  • N. Galtier M. Gouy C. Gautier (1996) ArticleTitleSEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny Comput. Appl. Biosci. 12 543–548 Occurrence Handle9021275 Occurrence Handle1:CAS:528:DyaK2sXhtlWktLw%3D

    PubMed  CAS  Google Scholar 

  • 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) ArticleTitleA draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science 296 92–100 Occurrence Handle11935018 Occurrence Handle1:CAS:528:DC%2BD38XivVSqtrw%3D Occurrence Handle10.1126/science.1068275

    Article  PubMed  CAS  Google Scholar 

  • T. Greb O. Clarenz E. Schafer D. Muller R. Herrero G. Schmitz K. Theres (2003) ArticleTitleMolecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation Genes Dev. 17 1175–1187 Occurrence Handle12730136 Occurrence Handle1:CAS:528:DC%2BD3sXjslGkt7s%3D Occurrence Handle10.1101/gad.260703

    Article  PubMed  CAS  Google Scholar 

  • S. Griffiths R.P. Dunford G. Coupland D.A. Laurie (2003) ArticleTitleThe evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis Plant Physiol. 131 1855–1867 Occurrence Handle12692345 Occurrence Handle1:CAS:528:DC%2BD3sXjt1Sqsbc%3D Occurrence Handle10.1104/pp.102.016188

    Article  PubMed  CAS  Google Scholar 

  • M.G. Heisler A. Atkinson Y.H. Bylstra R. Walsh D.R. Smyth (2001) ArticleTitleSPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein Development 128 1089–1098 Occurrence Handle11245574 Occurrence Handle1:CAS:528:DC%2BD3MXjtFOlt7o%3D

    PubMed  CAS  Google Scholar 

  • A. Ikeda M. Ueguchi-Tanaka Y. Sonoda H. Kitano M. Koshioka Y. Futsuhara M. Matsuoka J. Yamaguchi (2001) ArticleTitleSlender 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 Occurrence Handle11340177 Occurrence Handle1:CAS:528:DC%2BD3MXktVSlurk%3D Occurrence Handle10.1105/tpc.13.5.999

    Article  PubMed  CAS  Google Scholar 

  • In-depth view of structure, activity, and evolution of rice chromosome 10. 2003. Science 300: 1566–1569

  • D.H. Jeong S. An H.G. Kang S. Moon J.J. Han S. Park H.S. Lee K. An G. An (2002) ArticleTitleT-DNA insertional mutagenesis for activation tagging in rice Plant Physiol. 130 1636–1644 Occurrence Handle12481047 Occurrence Handle1:CAS:528:DC%2BD3sXktleg Occurrence Handle10.1104/pp.014357

    Article  PubMed  CAS  Google Scholar 

  • M.T. Juarez J.S. Kui J. Thomas B.A. Heller M.C. Timmermans (2004) ArticleTitleMicroRNA-mediated repression of rolled leaf1 specifies maize leaf polarity Nature 428 84–88 Occurrence Handle14999285 Occurrence Handle1:CAS:528:DC%2BD2cXhslCnsL8%3D Occurrence Handle10.1038/nature02363

    Article  PubMed  CAS  Google Scholar 

  • R.A. Kerstetter K. Bollman R.A. Taylor K. Bomblies R.S. Poethig (2001) ArticleTitleKANADI regulates organ polarity in Arabidopsis Nature 411 706–709 Occurrence Handle11395775 Occurrence Handle1:CAS:528:DC%2BD3MXksF2gur8%3D Occurrence Handle10.1038/35079629

    Article  PubMed  CAS  Google Scholar 

  • 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) ArticleTitleCollection, mapping, and annotation of over 28,000 cDNA clones from japonica rice Science 301 376–379 Occurrence Handle12869764 Occurrence Handle10.1126/science.1081288

    Article  PubMed  Google Scholar 

  • J.H. Kim D. Choi H. Kende (2003) ArticleTitleThe AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis Plant J. 36 94–104 Occurrence Handle12974814 Occurrence Handle1:CAS:528:DC%2BD3sXos12mt70%3D Occurrence Handle10.1046/j.1365-313X.2003.01862.x

    Article  PubMed  CAS  Google Scholar 

  • S. Kumar K. Tamura I.B. Jakobsen M. Nei (2001) ArticleTitleMEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 1244–1245 Occurrence Handle11751241 Occurrence Handle1:CAS:528:DC%2BD38XmtVCktQ%3D%3D Occurrence Handle10.1093/bioinformatics/17.12.1244

    Article  PubMed  CAS  Google Scholar 

  • D. Leister (2004) ArticleTitleTandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene Trends Genet. 20 116–122 Occurrence Handle15049302 Occurrence Handle1:CAS:528:DC%2BD2cXhsV2nu78%3D Occurrence Handle10.1016/j.tig.2004.01.007

    Article  PubMed  CAS  Google Scholar 

  • 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) ArticleTitleControl of tillering in rice Nature 422 618–621 Occurrence Handle12687001 Occurrence Handle1:CAS:528:DC%2BD3sXislCgtL0%3D Occurrence Handle10.1038/nature01518

    Article  PubMed  CAS  Google Scholar 

  • Z. Li T.L. Thomas (1998) ArticleTitlePEI1, an embryo-specific zinc finger protein gene required for heart-stage embryo formation in Arabidopsis Plant Cell 10 383–398 Occurrence Handle9501112 Occurrence Handle1:CAS:528:DyaK1cXitFGnt7c%3D Occurrence Handle10.1105/tpc.10.3.383

    Article  PubMed  CAS  Google Scholar 

  • J.R. McConnell J. Emery Y. Eshed N. Bao J. Bowman M.K. Barton (2001) ArticleTitleRole of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots Nature 411 709–713 Occurrence Handle11395776 Occurrence Handle1:CAS:528:DC%2BD3MXksF2ns7w%3D Occurrence Handle10.1038/35079635

    Article  PubMed  CAS  Google Scholar 

  • W. McGinnis M.S. Levine E. Hafen A. Kuroiwa W.J. Gehring (1984) ArticleTitleA conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes Nature 308 428–433 Occurrence Handle6323992 Occurrence Handle1:CAS:528:DyaL2cXhs12gsb4%3D Occurrence Handle10.1038/308428a0

    Article  PubMed  CAS  Google Scholar 

  • M. Mena B.A. Ambrose R.B. Meeley S.P. Briggs M.F. Yanofsky R.J. Schmidt (1996) ArticleTitleDiversification of C-function activity in maize flower development Science 274 1537–1540 Occurrence Handle8929416 Occurrence Handle1:CAS:528:DyaK28Xnt1ansb4%3D Occurrence Handle10.1126/science.274.5292.1537

    Article  PubMed  CAS  Google Scholar 

  • A. Miyao K. Tanaka K. Murata H. Sawaki S. Takeda K. Abe Y. Shinozuka K. Onosato H. Hirochika (2003) ArticleTitleTarget 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 Occurrence Handle12897251 Occurrence Handle10.1105/tpc.012559

    Article  PubMed  Google Scholar 

  • M.A. Moreno L.C. Harper R.W. Krueger S.L. Dellaporta M. Freeling (1997) ArticleTitleliguleless1 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis Genes Dev 11 616–628 Occurrence Handle9119226 Occurrence Handle1:CAS:528:DyaK2sXitVykurk%3D

    PubMed  CAS  Google Scholar 

  • N. Nagasawa M. Miyoshi Y. Sano H. Satoh H. Hirano H. Sakai Y. Nagato (2003) ArticleTitleSUPERWOMAN1 and DROOPING LEAF genes control floral organ identity in rice Development 130 705–718 Occurrence Handle12506001 Occurrence Handle1:CAS:528:DC%2BD3sXhslWjtbw%3D Occurrence Handle10.1242/dev.00294

    Article  PubMed  CAS  Google Scholar 

  • L. Parenicova S. Folter Particlede 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) ArticleTitleMolecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world Plant Cell 15 1538–1551 Occurrence Handle12837945 Occurrence Handle1:CAS:528:DC%2BD3sXlslWktb4%3D Occurrence Handle10.1105/tpc.011544

    Article  PubMed  CAS  Google Scholar 

  • 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) ArticleTitle‘Green revolution’ genes encode mutant gibberellin response modulators Nature 400 256–261 Occurrence Handle10421366 Occurrence Handle1:CAS:528:DyaK1MXkvFWltbg%3D Occurrence Handle10.1038/22307

    Article  PubMed  CAS  Google Scholar 

  • S. Rajani V. Sundaresan (2001) ArticleTitleThe Arabidopsis myc/bHLH gene ALCATRAZ enables cell separation in fruit dehiscence Curr. Biol. 11 1914–1922 Occurrence Handle11747817 Occurrence Handle1:CAS:528:DC%2BD38XisFCq Occurrence Handle10.1016/S0960-9822(01)00593-0

    Article  PubMed  CAS  Google Scholar 

  • 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) ArticleTitleArabidopsis transcription factors: genome-wide comparative analysis among eukaryotes Science 290 2105–2110 Occurrence Handle11118137 Occurrence Handle1:CAS:528:DC%2BD3cXptVyjtbk%3D Occurrence Handle10.1126/science.290.5499.2105

    Article  PubMed  CAS  Google Scholar 

  • J.L. Riechmann (2002) NoChapterTitle Meyerowitz CsaE (Eds) Transcriptional regulation: a genomic overview Amerian Society of Plant Biologists Rockville

    Google Scholar 

  • J.L. Riechmann E.M. Meyerowitz (1997) ArticleTitleMADS domain proteins in plant development Biol. Chem. 378 1079–1101 Occurrence Handle9372178 Occurrence Handle1:CAS:528:DyaK2sXmvFOju70%3D Occurrence Handle10.1515/bchm.1997.378.10.1079

    Article  PubMed  CAS  Google Scholar 

  • A.A. Salamov V.V. Solovyev (2000) ArticleTitleAb initio gene finding in Drosophila genomic DNA Genome Res. 10 516–522 Occurrence Handle10779491 Occurrence Handle1:CAS:528:DC%2BD3cXjtVKrs7Y%3D Occurrence Handle10.1101/gr.10.4.516

    Article  PubMed  CAS  Google Scholar 

  • 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) ArticleTitleThe genome sequence and structure of rice chromosome 1 Nature 420 312–316 Occurrence Handle12447438 Occurrence Handle1:CAS:528:DC%2BD38XovVektLw%3D Occurrence Handle10.1038/nature01184

    Article  PubMed  CAS  Google Scholar 

  • S. Sawa K. Watanabe K. Goto Y.G. Liu D. Shibata E. Kanaya E.H. Morita K. Okada (1999) ArticleTitleFILAMENTOUS 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 Occurrence Handle10323860 Occurrence Handle1:CAS:528:DyaK1MXjt1yiu74%3D

    PubMed  CAS  Google Scholar 

  • S. Schellmann A. Schnittger V. Kirik T. Wada K. Okada A. Beermann J. Thumfahrt G. Jurgens M. Hulskamp (2002) ArticleTitleTRIPTYCHON and CAPRICE mediate lateral inhibition during trichome and root hair patterning in Arabidopsis Embo. J. 21 5036–5046 Occurrence Handle12356720 Occurrence Handle1:CAS:528:DC%2BD38Xns1Cmsbs%3D Occurrence Handle10.1093/emboj/cdf524

    Article  PubMed  CAS  Google Scholar 

  • J. Schiefelbein (2003) ArticleTitleCell-fate specification in the epidermis: a common patterning mechanism in the root and shoot Curr. Opin. Plant Biol. 6 74–78 Occurrence Handle12495754 Occurrence Handle1:CAS:528:DC%2BD38XpsFegs7s%3D Occurrence Handle10.1016/S136952660200002X

    Article  PubMed  CAS  Google Scholar 

  • U. Schiefthaler S. Balasubramanian P. Sieber D. Chevalier E. Wisman K. Schneitz (1999) ArticleTitleMolecular 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 Occurrence Handle10500234 Occurrence Handle1:CAS:528:DyaK1MXmvVCmurw%3D Occurrence Handle10.1073/pnas.96.20.11664

    Article  PubMed  CAS  Google Scholar 

  • K. Schumacher T. Schmitt M. Rossberg G. Schmitz K. Theres (1999) ArticleTitleThe lateral suppressor (Ls) gene of tomato encodes a new member of the VHIID protein family Proc. Natl. Acad. Sci. USA 96 290–295 Occurrence Handle9874811 Occurrence Handle1:CAS:528:DyaK1MXjvV2guw%3D%3D Occurrence Handle10.1073/pnas.96.1.290

    Article  PubMed  CAS  Google Scholar 

  • M.P. Scott A.J. Weiner (1984) ArticleTitleStructural 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 Occurrence Handle6330741 Occurrence Handle1:CAS:528:DyaL2cXltVGis7Y%3D Occurrence Handle10.1073/pnas.81.13.4115

    Article  PubMed  CAS  Google Scholar 

  • P.S. Soltis D.E. Soltis M.W. Chase (1999) ArticleTitleAngiosperm phylogeny inferred from multiple genes as a tool for comparative biology Nature 402 402–404 Occurrence Handle10586878 Occurrence Handle1:CAS:528:DyaK1MXnvVykurg%3D Occurrence Handle10.1038/46528

    Article  PubMed  CAS  Google Scholar 

  • P.S. Soltis D.E. Soltis V. Savolainen P.R. Crane T.G. Barraclough (2002) ArticleTitleRate 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 Occurrence Handle11917101 Occurrence Handle1:CAS:528:DC%2BD38XivFShtLg%3D Occurrence Handle10.1073/pnas.032087199

    Article  PubMed  CAS  Google Scholar 

  • M. Suzuki C.Y. Kao S. Cocciolone D.R. McCarty (2001) ArticleTitleMaize VP1 complements Arabidopsis abi3 and confers a novel ABA/auxin interaction in roots Plant J. 28 409–418 Occurrence Handle11737778 Occurrence Handle1:CAS:528:DC%2BD38XmtVGhtg%3D%3D Occurrence Handle10.1046/j.1365-313X.2001.01165.x

    Article  PubMed  CAS  Google Scholar 

  • H. Takatsuji (1998) ArticleTitleZinc-finger transcription factors in plants Cell Mol. Life Sci. 54 582–596 Occurrence Handle9676577 Occurrence Handle1:CAS:528:DyaK1cXktFKkt7w%3D Occurrence Handle10.1007/s000180050186

    Article  PubMed  CAS  Google Scholar 

  • P.B. Talbert H.T. Adler D.W. Parks L. Comai (1995) ArticleTitleThe 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 Occurrence Handle7555701 Occurrence Handle1:CAS:528:DyaK2MXotF2mt7o%3D

    PubMed  CAS  Google Scholar 

  • G. Theissen A. Becker A. Di Rosa A. Kanno J.T. Kim T. Munster K.U. Winter H. Saedler (2000) ArticleTitleA short history of MADS-box genes in plants Plant Mol. Biol. 42 115–149 Occurrence Handle10688133 Occurrence Handle1:CAS:528:DC%2BD3cXht1Grsr8%3D Occurrence Handle10.1023/A:1006332105728

    Article  PubMed  CAS  Google Scholar 

  • G. Theodoris N. Inada M. Freeling (2003) ArticleTitleConservation and molecular dissection of ROUGH SHEATH2 and ASYMMETRIC LEAVES1 function in leaf development Proc. Natl. Acad. Sci. USA 100 6837–6842 Occurrence Handle12750468 Occurrence Handle1:CAS:528:DC%2BD3sXktlygtro%3D Occurrence Handle10.1073/pnas.1132113100

    Article  PubMed  CAS  Google Scholar 

  • C. Tian P. Wan S. Sun J. Li M. Chen (2004) ArticleTitleGenome-wide analysis of the GRAS gene family in rice and Arabidopsis Plant Mol. Biol. 54 519–532 Occurrence Handle15316287 Occurrence Handle1:CAS:528:DC%2BD2cXmslWnsLc%3D Occurrence Handle10.1023/B:PLAN.0000038256.89809.57

    Article  PubMed  CAS  Google Scholar 

  • 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)

  • G. Toledo-Ortiz E. Huq P.H. Quail (2003) ArticleTitleThe Arabidopsis basic/helix-loop-helix transcription factor family Plant Cell 15 1749–1770 Occurrence Handle12897250 Occurrence Handle1:CAS:528:DC%2BD3sXms1WlsLg%3D Occurrence Handle10.1105/tpc.013839

    Article  PubMed  CAS  Google Scholar 

  • M. Vandenbussche J. Zethof S. Royaert K. Weterings T. Gerats (2004) ArticleTitleThe duplicated B-class heterodimer model: whorl-specific effects and complex genetic interactions in Petunia hybrida flower development Plant Cell 16 741–754 Occurrence Handle14973163 Occurrence Handle1:CAS:528:DC%2BD2cXisFGkur4%3D Occurrence Handle10.1105/tpc.019166

    Article  PubMed  CAS  Google Scholar 

  • T. Wada T. Tachibana Y. Shimura K. Okada (1997) ArticleTitleEpidermal cell differentiation in Arabidopsis determined by a Myb homolog, CPC Science 277 1113–1116 Occurrence Handle9262483 Occurrence Handle1:CAS:528:DyaK2sXlsFSnsrw%3D Occurrence Handle10.1126/science.277.5329.1113

    Article  PubMed  CAS  Google Scholar 

  • R.L. Wang A. Stec J. Hey L. Lukens J. Doebley (1999) ArticleTitleThe limits of selection during maize domestication Nature 398 236–239 Occurrence Handle10094045 Occurrence Handle1:CAS:528:DyaK1MXitVGkt7g%3D Occurrence Handle10.1038/18435

    Article  PubMed  CAS  Google Scholar 

  • N. Wikstrom V. Savolainen M.W. Chase (2001) ArticleTitleEvolution of the angiosperms: calibrating the family tree Proc. R. Soc. Lond. B. Biol. Sci. 268 2211–2220 Occurrence Handle1:STN:280:DC%2BD3MrmvVKmtQ%3D%3D Occurrence Handle10.1098/rspb.2001.1782

    Article  CAS  Google Scholar 

  • K.H. Wolfe M. Gouy Y.W. Yang P.M. Sharp W.H. Li (1989) ArticleTitleDate of the monocot-dicot divergence estimated from chloroplast DNA sequence data Proc. Natl. Acad. Sci. USA 86 6201–6205 Occurrence Handle2762323 Occurrence Handle1:CAS:528:DyaL1MXltlSqsLY%3D Occurrence Handle10.1073/pnas.86.16.6201

    Article  PubMed  CAS  Google Scholar 

  • T. Yamaguchi N. Nagasawa S. Kawasaki M. Matsuoka Y. Nagato H.Y. Hirano (2004) ArticleTitleThe YABBY gene DROOPING LEAF regulates carpel specification and midrib development in Oryza sativa Plant Cell 16 500–509 Occurrence Handle14729915 Occurrence Handle1:CAS:528:DC%2BD2cXhsFKisL8%3D Occurrence Handle10.1105/tpc.018044

    Article  PubMed  CAS  Google Scholar 

  • W.C. Yang D. Ye J. Xu V. Sundaresan (1999) ArticleTitleThe SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein Genes Dev. 13 2108–2117 Occurrence Handle10465788 Occurrence Handle1:CAS:528:DyaK1MXmtValsb8%3D

    PubMed  CAS  Google Scholar 

  • 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) ArticleTitleA draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science 296 79–92 Occurrence Handle11935017 Occurrence Handle1:CAS:528:DC%2BD38XivVSqtr8%3D Occurrence Handle10.1126/science.1068037

    Article  PubMed  CAS  Google Scholar 

  • Q. Yuan S. Ouyang J. Liu B. Suh F. Cheung R. Sultana D. Lee J. Quackenbush C.R. Buell (2003) ArticleTitleThe TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists Nucleic Acids Res. 31 229–233 Occurrence Handle12519988 Occurrence Handle1:CAS:528:DC%2BD3sXhvFSnu74%3D Occurrence Handle10.1093/nar/gkg059

    Article  PubMed  CAS  Google Scholar 

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  1. Yuqing Xiong & Tieyan Liu

    Present address: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China

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  1. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China

    Chaoguang Tian, Shouhong Sun, Jiayang Li & Mingsheng Chen

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  1. Yuqing Xiong
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  2. Tieyan Liu
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Correspondence to Mingsheng Chen.

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Xiong, Y., Liu, T., Tian, C. et al. Transcription Factors in Rice: A Genome-wide Comparative Analysis between Monocots and Eudicots. Plant Mol Biol 59, 191–203 (2005). https://doi.org/10.1007/s11103-005-6503-6

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