Genome-wide identification and evolutionary analysis of the SBP-box gene family in castor bean.
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.
Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, China ; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, China.
Shu-Dong
SD
Zhang
Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, China ; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, China.
Li-Zhen
LZ
Ling
D017360:Arabidopsis / Q000235:genetics; D002367:Ricinus communis / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D017343:Genes, Plant; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005810:Multigene Family; D010802:Phylogeny; D014157:Transcription Factors / Q000235:genetics*
D014157:Transcription Factors