Comparative study of the SBP-box gene family in rice siblings

SBP-box genes are a class of plant-specific transcription factors which have a common DNA-binding domain(SBP-domain) with an unusual zinc-finger architecture. Many of the genes in this class are thought to play adevelopmental role and a few are involved in the determination of plant architecture. We have made acomparative study of these genes in the genomes of rice (Oryza sativa japonica and Oryza sativa indica) andits nine siblings using a recently proposed hybrid method for orthology and paralogy detection (HyPPO).According to HyPPO, the SBP-box proteins of rice siblings could be divided into twenty primary orthologousgroups on the basis of their overall sequence features. This contrasts with a much less number of groups foundin earlier work with other plant genomes using phylogenetic analysis of the SBP-domains only. The orthologous groups reported by HyPPO showed close correspondence in exon–intron structure and motif conservation. Comparison between different Oryza species revealed disparity in the maintenance of orthologousgenes which may result in their different developmental characteristics. Inclusion of the SBP-box proteins fromA. thaliana did not result in any change in the orthologous groups except for the A. thaliana proteins beingadded to some of the existing groups. The closer correspondence between the proteins in the primaryorthologous clusters is expected to help in a more reliable prediction of their functions. It is also expected toprovide better insight into the evolutionary history of this class of plant-specific proteins.