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Russian Journal of Plant Physiology

, Volume 57, Issue 2, pp 273–282 | Cite as

Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in grapevine

  • Y. WangEmail author
  • Z. Hu
  • Y. Yang
  • X. Chen
  • G. Chen
Research Papers

Abstract

The SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SBP) proteins form a family of transcriptional regulators, which are present exclusively in plants. Members of this family control processes such as flower development, sporogenesis, toxin resistance, control of GA levels, and response to copper. A genome-wide characterization of this family has not been conducted in a berry species, such as grapevine. Recent publication of the complete grapevine genome opens the possibility for an in depth analysis of the SBP-box gene family in grapevine. By screening the available databases, we identified 19 SBP-box genes with high sequence identity within the conserved SBP domain. An analysis of a complete set of SBP-box proteins in grapevine is presented, including their classification, gene structures, conserved motifs, and phylogenetic relationships. The grapevine SBP-box proteins can be classified into three groups (A, B, and C) based on their phylogenetic relationships with Arabidopsis SBP-box proteins. The expression patterns of the SBP-box genes were further investigated by searching against EST and microarray data. We found that the grapevine SBP-box genes were expressed primarily in flowers and fruit. The comparison of the SBP-box proteins of grapevine and tomato suggested that grapevine SBP-box genes might play an important role in fruit development.

Key words

Vitis vinifera SBP-box grapevine phylogenetic analysis EST expression profiling 

Abbreviations

EST

expressed sequence tag

MEME

Multiple EM (Expectation Maximization) for Motif Elicitation)

SBP

SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE

TF

transcription factor

TIGR

The Institute for Genomic Research

VvSBP

Vitis vinifera SBP

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References

  1. 1.
    Cardon, G.H., Hohmann, S., Nettesheim, K., Saedler, H., and Huijser, P., Functional Analysis of the Arabidopsis thaliana SBP-Box Gene SPL3: A Novel Gene Involved in the Floral Transition, Plant J., 1997, vol. 12, pp. 367–377.CrossRefPubMedGoogle Scholar
  2. 2.
    Cardon, G., Hohmann, S., Klein, J., Nettesheim, K., Saedler, H., and Huijser, P., Molecular Characterisation of the Arabidopsis SBP-Box Genes, Gene, 1999, vol. 237, pp. 91–104.CrossRefPubMedGoogle Scholar
  3. 3.
    Klein, J., Saedler, H., and 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., 1996, vol. 250, pp. 7–16.PubMedGoogle Scholar
  4. 4.
    Huijser, P., Klein, J., Lonnig, W.E., Meijer, H., Saedler, H., and Sommer, H., Bracteomania, an Inflorescence Anomaly, Is Caused by the Loss of Function of the MADS-Box Gene SQUAMOSA in Antirrhinum majus, EMBO J., 1992, vol. 11, pp. 1239–1249.Google Scholar
  5. 5.
    Yang, Z., Wang, X., Gu, S., Hu, Z., Xu, H., and Xu, C., Comparative Study of SBP-Box Gene Family in Arabidopsis and Rice, Gene, 2008, vol. 407, pp. 1–11.CrossRefPubMedGoogle Scholar
  6. 6.
    Guo, A.Y., Zhu, Q.H., Gu, X., Ge, S., Yang, J., and Luo, J., Genome-Wide Identification and Evolutionary Analysis of the Plant Specific SBP-Box Transcription Factor Family, Gene, 2008, vol. 418, pp. 1–8.CrossRefPubMedGoogle Scholar
  7. 7.
    Unte, U.S., Sorensen, A.M., Pesaresi, P., Gandikota, M., Leister, D., Saedler, H., and Huijser, P., SPL8, an SBP-Box Gene That Affects Pollen Sac Development in Arabidopsis, Plant Cell, 2003, vol. 15, pp. 1009–1019.CrossRefPubMedGoogle Scholar
  8. 8.
    Stone, J.M., Liang, X., Nekl, E.R., and Stiers, J.J., Arabidopsis AtSPL14, a Plant-Specific SBP-Domain Transcription Factor, Participates in Plant Development and Sensitivity to Fumonisin B1, Plant J., 2005, vol. 41, pp. 744–754.CrossRefPubMedGoogle Scholar
  9. 9.
    Zhang, Y., Schwarz, S., Saedler, H., and Huijser, P., SPL8, a Local Regulator in a Subset of Gibberellin-Mediated Developmental Processes in Arabidopsis, Plant Mol. Biol., 2007, vol. 63, pp. 429–439.CrossRefPubMedGoogle Scholar
  10. 10.
    Wang, H., Nussbaum-Wagler, T., Li, B., Zhao, Q., Vigouroux, Y., Faller, M., Bomblies, K., Lukens, L., and Doebley, J.F., The Origin of the Naked Grains of Maize, Nature, 2005, vol. 436, pp. 714–719.CrossRefPubMedGoogle Scholar
  11. 11.
    Manning, K., Tor, M., Poole, M., Hong, Y., Thompson, A.J., King, G.J., Giovannoni, J.J., and Seymour, G.B., A Naturally Occurring Epigenetic Mutation in a Gene Encoding an SBP-Box Transcription Factor Inhibits Tomato Fruit Ripening, Nat. Genet., 2006, vol. 38, pp. 948–952.CrossRefPubMedGoogle Scholar
  12. 12.
    Schwarz, S., Grande, A.V., Bujdoso, N., Saedler, H., and Huijser, P., The MicroRNA Regulated SBP-Box Genes SPL9 and SPL15 Control Shoot Maturation in Arabidopsis, Plant Mol. Biol., 2008, vol. 67, pp. 183–195.CrossRefPubMedGoogle Scholar
  13. 13.
    Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A., Cestaro, A., Pruss, D., Pindo, M., Fitzgerald, L.M., Vezzulli, S., Reid, J., Malacarme, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J.T., Perazzolli, M., Eldredge, G., Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C., Davenport, Ch., Dematte, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., Si-Ammour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev, V., Fawcett, J.A., Sterck, L., Vandepoele, K., Grando, S.M., Toppo, S., Moser, C., Lanchbury, J., Bodgen, R., Skolnick, M., Sgaramella, V., Bhathagar, S.K., Fontana, P., Gutin, A., van de Peer, Y., Salamini, F., and Voila, R., A High Quality Draft Consensus Sequence of the Genome of a Heterozygous grapevine Variety, PLoS ONE, 2007, vol. 2, p. e1326.CrossRefPubMedGoogle Scholar
  14. 14.
    Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg, S., Vitulo, N., Jubin, C., Vezzi, A., Legeai, F., Hugueney, P., Dasilva, C., Horner, D., Mica, E., Jublot, D., Poulain, J., Bruyere, C., Billault, A., Segurens, B., Gouyvenoux, M., Ugarte, E., Cattonaro, F., Anthouard, V., Vico, V., del Alaux, M., di Dumas, V., Felice, N., Paillard, S., Juman, I., Moroldo, M., Scalabrin, S., Canaguier, A., Le Clainche, I., Malacrida, G., Durand, E., Pesole, G., Laucou, V., Chatelet, P., Merdinoglu, D., Delledonne, M., Pezzotti, M., Lecharny, A., Scarpelli, C., Artiguenave, F., Pe, M.E., Valle, G., Morgante, M., Caboche, M., Adam-Blondon, A.F., Weissenbach, J., Quetier, F., and Wincker, P., The grapevine Genome Sequence Suggests Ancestral Hexaploidization in Major Angiosperm Phyla, Nature, 2007, vol. 449, pp. 463–467.CrossRefPubMedGoogle Scholar
  15. 15.
    Deluc, L.G., Grimplet, J., Wheatley, M.D., Tillett, R.L., Quilici, D.R., Osborne, C., Schooley, D.A., Schlauch, K.A., Cushman, J.C., and Cramer, G.R., Transcriptomic and Metabolite Analyses of Cabernet Sauvignon grapevine Berry Development, BMC Genomics, 2007, vol. 8, p. 429.CrossRefPubMedGoogle Scholar
  16. 16.
    Wise, R.P., Caldo, R.A., Hong, L., Shen, L., Cannon, E., and Dickerson, J.A., Barleybase/Plexdb: A Unified Expression Profiling Database for Plants and Plant Pathogens, Methods Mol. Biol., 2007, vol. 406, pp. 347–364.CrossRefPubMedGoogle Scholar
  17. 17.
    Adams, M.D., Kerlavage, A.R., Fleischmann, R.D., Fuldner, R.A., Bult, C.J., Lee, N.H., Kirkness, E.F., Weinstock, K.G., Gocayne, J.D., and White, O., Initial Assessment of Human Gene Diversity and Expression Patterns Based upon 83 Million Nucleotides of cDNA Sequence, Nature, 1995, vol. 377, pp. 3–174.PubMedGoogle Scholar
  18. 18.
    Quackenbush, J., Liang, F., Holt, I., Pertea, G., and Upton, J., The TIGR Gene Indices: Reconstruction and Representation of Expressed Gene Sequences, Nucleic Acids Res., 2000, vol. 28, pp. 141–145.CrossRefPubMedGoogle Scholar
  19. 19.
    Xie, K., Wu, C., and Xiong, L., Genomic Organization, Differential Expression, and Interaction of Squamosa Promoter-Binding-Like Transcription Factors and MicroRNA 156 in Rice, Plant Physiol., 2006, vol. 142, pp. 280–293.CrossRefPubMedGoogle Scholar
  20. 20.
    Schmid, M., Uhlenhaut, N.H., Godard, F., Demar, M., Bressan, R., Weigel, D., and Lohmann, J.U., Dissection of Floral Induction Pathways Using Global Expression Analysis, Development, 2003, vol. 130, pp. 6001–6012.CrossRefPubMedGoogle Scholar
  21. 21.
    Birkenbihl, R.P., Jach, G., Saedler, H., and Huijser, P., Functional Dissection of the Plant-Specific SBP-Domain: Overlap of the DNA-Binding and Nuclear Localization Domains, J. Mol. Biol., 2005, vol. 352, pp. 585–596.CrossRefPubMedGoogle Scholar
  22. 22.
    Vrebalov, J., Ruezinsky, D., Padmanabhan, V., White, R., Medrano, D., Drake, R., Schuch, W., and Giovannoni, J., A MADS-Box Gene Necessary for Fruit Ripening at the Tomato Ripening-Inhibitor (Rin) Locus, Science, 2002, vol. 296, pp. 343–346.CrossRefPubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2010

Authors and Affiliations

  1. 1.College of BioengineeringChongqing UniversityChongqingChina
  2. 2.Beijing Research Center of Agro-BiotechnologyBeijingChina

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