Dataset Information

Genome-wide identification and evolutionary analysis of the SBP-box gene family in castor bean.

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.

SUBMITTER: Zhang SD

PROVIDER: S-EPMC3899293 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Genome-wide identification and evolutionary analysis of the SBP-box gene family in castor bean.

Zhang Shu-Dong SD Ling Li-Zhen LZ

PloS one 20140122 1

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 bi ...[more]

PMID: 24466202

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Project description:BACKGROUND:SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box genes encode a family of plant-specific transcription factors (TFs) that play important roles in many growth and development processes including phase transition, leaf initiation, shoot and inflorescence branching, fruit development and ripening etc. The SBP-box gene family has been identified and characterized in many species, but has not been well studied in Petunia, an important ornamental genus. RESULTS:We identified 21 putative SPL genes of Petunia axillaris and P. inflata from the reference genome of P. axillaris N and P. inflata S6, respectively, which were supported by the transcriptome data. For further confirmation, all the 21 genes were also cloned from P. hybrida line W115 (Mitchel diploid). Phylogenetic analysis based on the highly conserved SBP domains arranged PhSPLs in eight groups, analogous to those from Arabidopsis and tomato. Furthermore, the Petunia SPL genes had similar exon-intron structure and the deduced proteins contained very similar conserved motifs within the same subgroup. Out of 21 PhSPL genes, fourteen were predicted to be potential targets of PhmiR156/157, and the putative miR156/157 response elements (MREs) were located in the coding region of group IV, V, VII and VIII genes, but in the 3'-UTR regions of group VI genes. SPL genes were also identified from another two wild Petunia species, P. integrifolia and P. exserta, based on their transcriptome databases to investigate the origin of PhSPLs. Phylogenetic analysis and multiple alignments of the coding sequences of PhSPLs and their orthologs from wild species indicated that PhSPLs were originated mainly from P. axillaris. qRT-PCR analysis demonstrated differential spatiotemperal expression patterns of PhSPL genes in petunia and many were expressed predominantly in the axillary buds and/or inflorescences. In addition, overexpression of PhSPL9a and PhSPL9b in Arabidopsis suggested that these genes play a conserved role in promoting the vegetative-to-reproductive phase transition. CONCLUSION:Petunia genome contains at least 21 SPL genes, and most of the genes are expressed in different tissues. The PhSPL genes may play conserved and diverse roles in plant growth and development, including flowering regulation, leaf initiation, axillary bud and inflorescence development. This work provides a comprehensive understanding of the SBP-box gene family in Petunia and lays a significant foundation for future studies on the function and evolution of SPL genes in petunia.

Dataset Information

Genome-wide identification and evolutionary analysis of the SBP-box gene family in castor bean.

Publications

Genome-wide identification and evolutionary analysis of the SBP-box gene family in castor bean.

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