Transcriptome-wide identification and expression analysis of chrysanthemum SBP-like transcription factors

• 12 SPL genes were isolated and characterized in chrysanthemum.
• Conserved motifs in the SBP-box proteins were shared by Arabidopsis and chrysanthemum.
• 6 CmSPLs contained a miR156 target site, while 5 CmSPLs were targeted by miR157.
• The hormone and stress treatments arouse the expression of 12 CmSPLs variously.

SQUAMOSA promoter-binding protein (SBP) transcription factors are known to function in a number of processes in plants. Here, we have characterized twelve SBP-like (SPL) genes in the important ornamental species chrysanthemum (Chrysanthemum morifolium). A total of twelve distinct sequences were isolated and amplified based on transcriptomic sequences. Phylogenetic analysis identified two pairs of orthologous proteins for Arabidopsis and chrysanthemum and two pairs of paralogous proteins in chrysanthemum. Conserved motifs in the SPL proteins shared by Arabidopsis and chrysanthemum were scanned using MEME. A bioinformatics analysis revealed that six of these genes contained a miR156 target site, while five CmSPLs were targeted by miR157. Moreover, we used 5′ RLM-RACE to map the cleavage sites in CmSPL2 and CmSPL3. The expression of these twelve genes in response to a variety of phytohormone treatments and abiotic stresses was characterized. This work improves our understanding of the various functions of SPL gene family members in the stress response.