Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family

Gene. 2008 Jul 15;418(1-2):1-8. doi: 10.1016/j.gene.2008.03.016. Epub 2008 Apr 9.


We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Conserved Sequence
  • Evolution, Molecular*
  • Genes, Plant*
  • Genome, Plant*
  • MicroRNAs / analysis*
  • Multigene Family*
  • Phylogeny
  • Transcription Factors*
  • Zinc Fingers


  • MicroRNAs
  • Transcription Factors