Abstract
Genes in the SQUAMOSA promoter-binding-protein (SBP-box) gene family encode transcriptional regulators and perform a variety of regulatory functions that involved in the developmental and physiological processes of plants. In this study, a comprehensive computational analysis identified 15 candidates of the SBP-box gene family in the castor bean (Ricinus communis). The phylogenetic and domain analysis indicated that these genes were divided into two groups (group I and II). The group II was a big branch and was further classified into three subgroups (subgroup II-1 to 3) based on the phylogeny, gene structures and conserved motifs. It was observed that the genes of subgroup II-1 had distinct evolutionary features from those of the other two subgroups, however, were more similar to those of group I. Therefore, we inferred that group I and subgroup II-1 might retain ancient signals, whereas the subgroup II-2 and 3 exhibited the divergence during evolutionary process. Estimation of evolutionary parameters (dN and dN/dS) further supported our hypothesis. At first, the group I was more constrained by strong purifying selection and evolved slowly with a lower substitution rate than group II. As regards the three subgroups, subgroup II-1 had the lowest rate of substitution and was under strong purifying selection. By contrast, subgroups II-2 and 3 evolved more rapidly and experienced less purifying selection. These results indicated that the different evolutionary rates and selection strength caused the different evolutionary patterns of the members of SBP-box genes in castor bean. Taken together, these results provide better insights into understanding evolutionary divergence of the members of SBP-box gene family in castor bean and provide a guide for future functional diverse analyses of this gene family.
Highlights
Precise and coordinate gene expression is essential for organism growth and development
Identification of SBP-box genes in castor bean To identify the SBP-box genes present in the castor bean, we used multiple BLAST algorithms to compare against the genome and protein data sets, using the representative SBP domains of Arabidopsis for each subgroup as our query
Following the removal of redundant sequences and SMART [18] analysis, we identified at least 15 putative SPL genes in the castor bean genome; in the absence of an existing nomenclature for them, we used the gene model and locus as identifiers (Table 1)
Summary
Precise and coordinate gene expression is essential for organism growth and development. Each member of this family contains a highly conserved DNAbinding domain (SQUAMOSA promoter-binding-protein (SBP) domain) with two separate zinc-binding sites (one zinc finger is C3H or C4, and the other is C2HC [4]) These SPL genes are known to have important functions in the transcriptional regulation of a variety of biological processes related to growth and development, and in controlling various responses to environmental stimuli [5]. A total of 15 SPL genes was identified using BLAST to search genome and protein sequence databases An overview of this gene family is presented, including the gene structures, phylogeny, and conserved motifs found in the castor bean. We discuss the relationship between the substitution rate and the expression level and protein length of SPL genes
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