Alvarez-Buylla ER, Liljegren SJ, Pelaz S, Gold SE, Burgeff C, Ditta GS, Vergara-Silva F, Yanofsky MF. MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes. Plant J. 2000;24(4):457–66.
Article
PubMed
CAS
Google Scholar
Zhang H, Forde BG. An Arabidopsis MADS box gene that controls nutrient-induced changes in root architecture. Science. 1998;279(5349):407–9.
Article
PubMed
CAS
Google Scholar
Alvarez-Buylla ER, Pelaz S, Liljegren SJ, Gold SE, Burgeff C, Ditta GS, De Pouplana LR, Martínez-Castilla L, Yanofsky MF. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc Natl Acad Sci. 2000;97(10):5328–33.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ng M, Yanofsky MF. Function and evolution of the plant MADS-box gene family. Nat Rev Genet. 2001;2(3):186–95.
Article
PubMed
CAS
Google Scholar
Kaufmann K, Melzer R, Theissen G. MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants. Gene. 2005;347(2):183–98.
Article
PubMed
CAS
Google Scholar
Yang Y, Jack T. Defining subdomains of the K domain important for protein-protein interactions of plant MADS proteins. Plant Molecular Biology. 2004;55(1):45–59.
Article
PubMed
CAS
Google Scholar
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. 2004;101(7):1910–1915.
Article
PubMed
CAS
PubMed Central
Google Scholar
Parenicová L, de Folter S, Kieffer M, Horner DS, Favalli C, Busscher J, Cook HE, Ingram RM, Kater MM, Davies B. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis new openings to the MADS world. Plant Cell. 2003;15(7):1538–51.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sanda SL, Amasino RM. Interaction ofFLC and late-flowering mutations inArabidopsis thaliana. Mol Gen Genet MGG. 1996;251(1):69–74.
PubMed
CAS
Google Scholar
Hartmann U, Höhmann S, Nettesheim K, Wisman E, Saedler H, Huijser P. Molecular cloning of SVP: a negative regulator of the floral transition in Arabidopsis. Plant J. 2000;21(4):351–60.
Article
PubMed
CAS
Google Scholar
Moon J, Suh SS, Lee H, Choi KR, Hong CB, Paek NC, Kim SG, Lee I. The SOC1 MADS-box gene integrates vernalization and gibberellin signals for flowering in Arabidopsis. Plant J. 2003;35(5):613–23.
Article
PubMed
CAS
Google Scholar
Mandel MA, Gustafson-Brown C, Savidge B, Yanofsky MF. Molecular characterization of the Arabidopsis floral homeotic gene APETALA1. Nature. 1992;360(6401):273–7.
Article
PubMed
CAS
Google Scholar
Gu Q, Ferrándiz C, Yanofsky MF, Martienssen R. The FRUITFULL MADS-box gene mediates cell differentiation during Arabidopsis fruit development. Development. 1998;125(8):1509–17.
PubMed
CAS
Google Scholar
Liljegren SJ, Ditta GS, Eshed Y, Savidge B, Bowman JL, Yanofsky MF. SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature. 2000;404(6779):766–70.
Article
PubMed
CAS
Google Scholar
Ma H. The ABCs of floral evolution. Cell. 2000;101(1):5–8.
Article
PubMed
CAS
Google Scholar
Riechmann JL, Meyerowitz EM. MADS domain proteins in plant development. Biological Chemistry. 1997;378(10):1079–1101.
PubMed
CAS
Google Scholar
Nesi N, Debeaujon I, Jond C, Stewart AJ, Jenkins GI, Caboche M, Lepiniec L. The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat. Plant Cell. 2002;14(10):2463–79.
Article
PubMed
PubMed Central
CAS
Google Scholar
Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, Kapoor S. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics. 2007;8(1):242.
Article
PubMed
PubMed Central
CAS
Google Scholar
Theissen G, Becker A, Di RA, Kanno A, Kim JT, Münster T, Winter KU, Saedler H. A short history of MADS-box genes in plants. Plant Molecular Biology. 2000;42(1):115–149.
Article
PubMed
CAS
Google Scholar
Yanofsky MF, Ma H, Bowman JL, Drews GN, Feldmann KA, Meyerowitz EM. The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature. 1990;346(6279):35–9.
Article
PubMed
CAS
Google Scholar
Weigel D, Meyerowitz EM. The ABCs of floral homeotic genes. Cell. 1994;78(2):203–9.
Article
PubMed
CAS
Google Scholar
Masiero S, Colombo L, Grini PE, Schnittger A, Kater MM. The emerging importance of type I MADS box transcription factors for plant reproduction. Plant Cell. 2011;23(3):865–72.
Article
PubMed
PubMed Central
CAS
Google Scholar
Clark LG, Londoño X, Ruiz-Sanchez E. Bamboo Taxonomy and Habitat. Springer International Publishing, 2015.
Google Scholar
Yuan JL, Yue JJ, Gu XP, Lin CS. Flowering of Woody bamboo in tissue culture systems. Front Plant Sci. 2017;8:1589.
Isagi Y, Shimada K, Kushima H, Tanaka N, Nagao A, Ishikawa T, Onodera H, Watanabe S. Clonal structure and flowering traits of a bamboo [Phyllostachys pubescens (mazel) Ohwi] stand grown from a simultaneous flowering as revealed by AFLP analysis. Mol Ecol. 2004;13(7):2017–21.
Article
PubMed
CAS
Google Scholar
Wong KM. Flowering, fruiting and germination of the bamboo Schizostachyum zollingeri in Perlis. Malays Forester. 1981;44(4):453–63.
Google Scholar
Campbell J. Bamboo flowering patterns:a global view with special reference to East Asia. J Am Bamboo Soc. 1985;6:17–35.
Google Scholar
Troup RS, Troup RS. The silviculture of Indian trees. Published under the authority of his Majesty’s secretary of state for India in council. Cesk Pediatr. 1921;12(1):1–12.
Google Scholar
Keeley JE, Bond WJ. Mast flowering and Semelparity in bamboos: the bamboo fire cycle hypothesis. Am Nat. 1999;154(3):383.
Article
PubMed
Google Scholar
Lin EP, Peng HZ, Jin QY, Deng MJ, Li T, Xiao XC, Hua XQ, Wang KH, Bian HW, Han N. Identification and characterization of two bamboo ( Phyllostachys praecox ) AP1 / SQUA- like MADS-box genes during floral transition. Planta. 2009;231(1):109–20.
Article
PubMed
CAS
Google Scholar
Shih MC, Chou ML, Yue JJ, Hsu CT, Chang WJ, Ko SS, Liao DC, Huang YT, Chen JJ, Yuan JL. BeMADS1 is a key to delivery MADSs into nucleus in reproductive tissues- De novo characterization of Bambusa edulis transcriptome and study of MADS genes in bamboo floral development. BMC Plant Biol. 2014;14(1):179.
Article
PubMed
PubMed Central
Google Scholar
Gao J, Zhang Y, Zhang C, Qi F, Li X, Mu S, Peng Z. Characterization of the floral transcriptome of Moso bamboo (Phyllostachys edulis) at different flowering developmental stages by transcriptome sequencing and RNA-Seq analysis. PLoS One. 2014;9(6):e98910.
Article
PubMed
PubMed Central
Google Scholar
Wei B, Zhang R-Z, Guo J-J, Liu D-M, Li A-L, Fan R-C, Mao L, Zhang X-Q. Genome-wide analysis of the MADS-box gene family in Brachypodium distachyon. PLoS One. 2014;9(1):e84781.
Article
PubMed
PubMed Central
CAS
Google Scholar
Solovyev V, Kosarev P, Seledsov I, Vorobyev D. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 2006;7(Suppl 1):1–12.
Article
PubMed
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–52.
Article
PubMed
PubMed Central
CAS
Google Scholar
Milne I, Stephen G, Bayer M, Cock PJ, Pritchard L, Cardle L, Shaw PD, Marshall D. Using tablet for visual exploration of second-generation sequencing data. Brief Bioinform. 2013;14(2):193–202.
Article
PubMed
CAS
Google Scholar
Sheen J. Signal transduction in maize and Arabidopsis mesophyll protoplasts. Plant Physiol. 2001;127(4):1466.
Article
PubMed
PubMed Central
CAS
Google Scholar
Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33(2):511–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Letunic I, Doerks T, Bork P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 2015;43(D1):D257–60.
Article
PubMed
CAS
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(suppl_2):W202–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schultz J, Milpetz F, Bork P, Ponting CP. SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci. 1998;95(11):5857–64.
Article
PubMed
CAS
PubMed Central
Google Scholar
Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 2012;40(Database issue):302–5.
Article
CAS
Google Scholar
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30(1):325.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fan C, Ma J, Guo Q, Li X, Wang H, Lu M. Selection of reference genes for quantitative real-time PCR in bamboo (Phyllostachys edulis). PLoS One. 2013;8(2):e56573.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhao H, Lou Y, Sun H, Li L, Wang L, Dong L, Gao Z. Transcriptome and comparative gene expression analysis of Phyllostachys edulisin response to high light. BMC Plant Biology. 2016;16(1):34.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhao T, Ni Z, Dai Y, Yao Y, Nie X, Sun Q. Characterization and expression of 42 MADS-box genes in wheat (Triticum aestivum L.). Mol Gen Genomics. 2006;276(4):334–50.
Article
CAS
Google Scholar
Chen S, Songkumarn P, Liu J, Wang GL. A versatile zero background T-vector system for gene cloning and functional genomics. Plant Physiol. 2009;150(3):1111–21.
Article
PubMed
PubMed Central
CAS
Google Scholar
Clough SJ, Bent AF. Floral dip: a simplified method for agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J Cell Mol Biol. 1998;16(6):735–43.
Article
CAS
Google Scholar
Henschel K, Kofuji R, Hasebe M, Saedler H, Münster T, Theißen G. Two ancient classes of MIKC-type MADS-box genes are present in the moss Physcomitrella patens. Mol Biol Evol. 2002;19(6):801–14.
Article
PubMed
CAS
Google Scholar
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573.
Article
PubMed
PubMed Central
CAS
Google Scholar
Folter SD, Angenent GC. Trans meets cis in MADS science. Trends Plant Sci. 2006;11(5):224–31.
Article
PubMed
CAS
Google Scholar
Khan MR, Hu J, Ali GM. Reciprocal loss of CArG-boxes and auxin response elements drives expression divergence of MPF2-like MADS-box genes controlling Calyx inflation. PLoS One. 2012;7(8):e42781.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gregis V, Sessa A, Dorca-Fornell C, Kater MM. The Arabidopsis floral meristem identity genes AP1, AGL24 and SVP directly repress class B and C floral homeotic genes. Plant J. 2010;60(4):626–37.
Article
CAS
Google Scholar
Torti S, Fornara F. AGL24 acts in concert with SOC1 and FUL during Arabidopsis floral transition. Plant Signal Behav. 2012;7(10):1251–4.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gregis V, Sessa A, Colombo L, Kater MM. AGL24, SHORT VEGETATIVE PHASE, and APETALA1 Rebundantly control AGAMOUS during early stages of flower development in Arabidopsis. Plant Cell. 2006;18(6):1373.
Article
PubMed
PubMed Central
CAS
Google Scholar
V G AS, D-F C, MM K. The Arabidopsis floral meristem identity genes AP1, AGL24 and SVP directly repress class B and C floral homeotic genes. Plant J. 2009;60(4):626–37.
Article
CAS
Google Scholar
Gramzow L, Weilandt L, Theißen G. MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants. Ann Bot. 2014;114(7):1407.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gramzow L, Ritz MS, Theißen G. On the origin of MADS-domain transcription factors. Trends Genet. 2010;26(4):149–53.
Article
PubMed
CAS
Google Scholar
Leseberg CH, Li A, Kang H, Duvall M, Mao L. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa. Gene. 2006;378:84–94.
Article
PubMed
CAS
Google Scholar
Kapazoglou A, Engineer C, Drosou V, Kalloniati C, Tani E, Tsaballa A, Kouri ED, Ganopoulos I, Flemetakis E, Tsaftaris AS. The study of two barley type I-like MADS-box genes as potential targets of epigenetic regulation during seed development. BMC Plant Biol. 2012;12(1):166.
Article
PubMed
PubMed Central
CAS
Google Scholar
Peng Z, Lu Y, Li L, Zhao Q, Feng Q, Gao Z, Lu H, Hu T, Yao N, Liu K. The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet. 2013;45(4):456–61.
Article
PubMed
CAS
Google Scholar
Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund CA, Mayer KF. Sequence composition and genome organization of maize. Proc Natl Acad Sci U S A. 2004;101(40):14349–54.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007;449(7161):463–7.
Article
PubMed
CAS
Google Scholar
Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497(7451):579–84.
Article
PubMed
CAS
Google Scholar
Finnegan DJ. Eukaryotic transposable elements and genome evolution. Trends Genet. 1989;5:103–7.
Article
PubMed
CAS
Google Scholar
Zhou M, Hu B, Zhu Y. Genome-wide characterization and evolution analysis of long terminal repeat retroelements in moso bamboo ( Phyllostachys edulis ). Tree Genet Genomes. 2017;13(2):43.
Article
Google Scholar
Ma J, SanMiguel P, Lai J, Messing J, Bennetzen JL. DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes. Genetics. 2005;170(3):1209–20.
Article
PubMed
PubMed Central
CAS
Google Scholar
SanMiguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z. Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996;274(5288):765–8.
Article
PubMed
CAS
Google Scholar
Bowman JL, Drews GN, Meyerowitz EM. Expression of the Arabidopsis floral homeotic gene AGAMOUS is restricted to specific cell types late in flower development. Plant Cell. 1991;3(8):749–58.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mizukami Y, Ma H. Ectopic expression of the floral homeotic gene AGAMOUS in transgenic Arabidopsis plants alters floral organ identity. Cell. 1992;71(1):119–31.
Article
PubMed
CAS
Google Scholar
Theißen G, Saedler H. Plant biology: floral quartets. Nature. 2001;409(6819):469–71.
Article
PubMed
Google Scholar
Theißen G, Kim JT, Saedler H. Classification and phylogeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes. J Mol Evol. 1996;43(5):484–516.
Article
PubMed
Google Scholar
Gao XC, Liang WQ, Yin CS, Ji SM, Wang HM, Xiao S, Guo CC, Kong HZ, Xue HW, Zhang DB. The SEPALLATA-like gene OsMADS34 is required for rice inflorescence and spikelet development. Plant Physiol. 2010;153(2):728–40.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liu C, Xi W, Shen L, Tan C, Yu H. Regulation of floral patterning by flowering time genes. Dev Cell. 2009;16(5):711–22.
Article
PubMed
Google Scholar
Yu H, Xu Y, Tan EL, Kumar PP. AGAMOUS-LIKE 24, a dosage-dependent mediator of the flowering signals. Proc Natl Acad Sci U S A. 2002;99(25):16336–41.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liu C, Chen H, Er HL, Soo HM, Kumar PP, Han JH, Liou YC, Yu H. Direct interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis. Development. 2008;135(8):1481.
Article
PubMed
CAS
Google Scholar
Lee JH, Yoo SJ, Park SH, Hwang I, Lee JS, Ahn JH. Role of SVP in the control of flowering time by ambient temperature in Arabidopsis. Genes Dev. 2007;21(4):397.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liu C, Zhou J, Brachadrori K, Yalovsky S, Ito T, Yu H. Specification of Arabidopsis floral meristem identity byrepression of flowering time genes. Development. 2007;134(10):1901.
Article
PubMed
CAS
Google Scholar
Lee JH, Park SH, Ji HA. Functional conservation and diversification between rice OsMADS22/OsMADS55 and Arabidopsis SVP proteins. Plant Sci. 2012;185-186:97–104.
Article
PubMed
CAS
Google Scholar
Pelaz S, Ditta GS, Baumann E, Wisman E, Yanofsky MF. B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature. 2000;405(6783):200.
Article
PubMed
CAS
Google Scholar
Peña L, Martíntrillo M, Juárez J, Pina JA, Navarro L, Martínezzapater JM. Constitutive expression of Arabidopsis LEAFY or APETALA1 genes in citrus reduces their generation time. Nat Biotechnol. 2001;19(3):263–7.
Article
PubMed
Google Scholar
Goto K. Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature. 2001;409(6819):525.
Article
PubMed
Google Scholar
Kramer EM, Jaramillo MA, Di SV. Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms. Genetics. 2004;166(2):1011–23.
Article
PubMed
PubMed Central
CAS
Google Scholar