, Volume 235, Issue 6, pp 1171–1184 | Cite as

Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato

  • María Salinas
  • Shuping Xing
  • Susanne Höhmann
  • Rita Berndtgen
  • Peter HuijserEmail author
Original Article


SBP-box genes represent transcription factors ubiquitously found in the plant kingdom and recognized as important regulators of many different aspects of plant development. In this study, 15 SBP-box gene family members were identified in tomato and analyzed with respect to their genomic organization and other structural features. Phylogenetic reconstruction based on the DNA-binding SBP-domain, allowed the classification of the SlySBP proteins into eight groups representing clear orthologous relationships to family members of other flowering plants and the moss Physcomitrella. In order to have a better understanding of their possible function in the development of a fleshy-fruit species like tomato, the mRNA expression levels of all SlySBP genes were quantified in vegetative and reproductive organs of plants, at different stages of growth. As transcripts of ten SlySBP genes were found to carry putative miR156- and miR157-response elements, the expression levels of the corresponding microRNAs were determined as well, revealing different patterns of expression. In addition, eight putative miR156 and four miR157 encoding loci could be identified in the tomato genome, four of them forming a polycistronic cluster. Whereas miR156 and miR157 levels were highest in seedlings, leaves and anthers of young flowers, most miR156-targeted SlySBP genes were found to be expressed in young inflorescences and during fruit development and ripening, suggesting a particularly important role during tomato reproductive growth. The data presented provide a basis for future clarification of the various functions that SBP-box gene family members play in tomato growth and development.


Gene expression miR156 Phylogeny SBP-box gene Solanum SQUAMOSA promoter binding protein Transcription factor 



Amino acid(s)


DNA complementary to RNA


Expressed sequence tag




MicroRNA responsive element


Million years


SQUAMOSA promoter binding protein


SQUAMOSA promoter binding protein-like


Untranslated region

Supplementary material

425_2011_1565_MOESM1_ESM.pdf (1.3 mb)
Supplementary material 1 (PDF 1301 kb)
425_2011_1565_MOESM2_ESM.txt (209 kb)
Supplementary material 2 (TXT 209 kb)


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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • María Salinas
    • 1
    • 2
  • Shuping Xing
    • 1
  • Susanne Höhmann
    • 1
  • Rita Berndtgen
    • 1
  • Peter Huijser
    • 1
    Email author
  1. 1.Department of Molecular Plant GeneticsMax Planck Institute for Plant Breeding ResearchCologneGermany
  2. 2.Departamento de Biología Aplicada, Área de GenéticaUniversidad de AlmeríaAlmeríaSpain

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