Abstract
BackgroundSquamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. Nevertheless, the evolutionary patterns of SBP-box genes and evolutionary forces driving them are still not well understood.Methods104 SBP-box gene candidates of five representative land plants were obtained from Phytozome database (v10.3). Phylogenetic combined with gene structure analyses were used to identify SBP-box gene lineages in land plants. Gene copy number and the sequence and structure features were then compared among these different SBP-box lineages. Selection analysis, relative rate tests and expression divergence were finally used to interpret the evolutionary relationships and divergence of SBP-box genes in land plants.ResultsWe investigated 104 SBP-box genes from moss, Arabidopsis, poplar, rice, and maize. These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis. Interestingly, subgroup II-1 genes have similar sequence and structural features to group I genes, whereas subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation. Further analyses indicate that subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes, just as group I genes do when compared to II genes. Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection. These results suggest that group I and subgroup II-1 genes under strong selective constraint are conserved. By contrast, subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation, which might contribute to morphological diversifications of land plants.ConclusionsOur results indicate that different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants, providing a guide for future functional diversity analyses of these genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1998-y) contains supplementary material, which is available to authorized users.
Highlights
Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis
Phylogenetic analysis of SBP-box genes in land plants Phylogenetic reconstruction was performed using neighbor-joining (NJ) approaches with JTT and P-distance models based on full-length protein sequences, which resulted in generally similar topologies
Sequence and structural characteristics of SBP-box genes We found that the sequence and structural features of subgroup II-1 SBP-box genes were highly similar to group I genes, groups II-1 and II-2 were sister in the phylogenetic tree (Fig. 1a)
Summary
Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. The differential regulation of SBP-box genes by two miRNA families provides an interesting example of the functions that these genes exhibit during land plant development; e.g., the low-level expression of SBP-box genes in an miR156-overexpression mutant prolonged the juvenile phase in maize [13] and Arabidopsis [14]. These studies suggest that land plant SBP-box genes have diverged and are functionally diverse. Our long-term research questions are: What evolutionary forces drive the divergence of SBP-box genes in land plants? Do these genes evolve under the same constraints and at the same rate?
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
