Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs

Abstract

SQUAMOSA PROMOTER BINDING PROTEIN-LIKEs (SPLs) encode plant-specific transcription factors that regulate plant growth and development, stress response, and metabolite accumulation. However, there is limited information on Scutellaria baicalensis SPLs. In this study, 14 SbSPLs were identified and divided into 8 groups based on phylogenetic relationships. SbSPLs in the same group had similar structures. Abscisic acid-responsive (ABRE) and MYB binding site (MBS) cis-acting elements were found in the promoters of 8 and 6 SbSPLs. Segmental duplications and transposable duplications were the main causes of SbSPL expansion. Expression analysis based on transcriptional profiling showed that SbSPL1, SbSPL10, and SbSPL13 were highly expressed in roots, stems, and flowers, respectively. Expression analysis based on quantitative real-time polymerase chain reaction (RT‒qPCR) showed that most SbSPLs responded to low temperature, drought, abscisic acid (ABA) and salicylic acid (SA), among which the expression levels of SbSPL7/9/10/12 were significantly upregulated in response to abiotic stress. These results indicate that SbSPLs are involved in the growth, development and stress response of S. baicalensis. In addition, 8 Sba-miR156/157 s were identified, and SbSPL1-5 was a potential target of Sba-miR156/157 s. The results of target gene prediction and coexpression analysis together indicated that SbSPLs may be involved in the regulation of L-phenylalanine (L-Phe), lignin and jasmonic acid (JA) biosynthesis. In summary, the identification and characterization of the SbSPL gene family lays the foundation for functional research and provides a reference for improved breeding of S. baicalensis stress resistance and quality traits.

Keywords: Expression pattern; Genetic and evolutionary information; Scutellaria baicalensis SPL transcription factor.

Fig. 1

Phylogenetic analysis of S. baicalensis and A. thaliana SPLs. Circles of different sizes and colors indicate the magnitude of the bootstrap value. The 8 main branches are individually marked with colored ranges

Fig. 2

Phylogenetic relationships, conserved motif composition and gene structure. A Phylogenetic tree. B Motif pattern of SbSPLs. The 10 colored boxes represent 10 different motifs, and their positions represent the positions on the protein. C Gene structure. CDS and introns are represented by green rectangles and black single lines, respectively

Fig. 3

Prediction of cis-acting elements in the SbSPL promoter. The gradient color in the cell represents the number

Fig. 4

Collinearity analysis of SbSPLs. The short lines of different colors inside the circle represent different gene duplication events, in which the short red lines represent proximal repeats; the short orange lines represent fragment repeats; the short green lines represent transposition repeats; and the short purple lines represent tandem repeats (none)

Fig. 5

Synteny analysis of SPLs between S. baicalensis and A. thaliana (A), S. lycopersicum (B), S. bowleyana (C), S. bicolor (D), O. sativa (E), and Z. mays (F). Syntenic gene pairs are highlighted with red lines. Chromosomes are arranged in ascending order from left to right, with numbering omitted

Fig. 6

Expression levels of SbSPLs in 4 tissues. In cells, orange indicates high expression, and blue indicates low expression

Fig. 7

Expression pattern of SbSPLs under abiotic stress and hormone treatment. Analysis of SbSPL expression levels under 4 °C (A), PEG (B), SA (C) and ABA (D) treatments. Different letters represent significantly different expression levels in the same treatment and gene at different times

Fig. 8

Multiple sequence alignment of the reverse complementary sequences of Sba-miR156/157 and SbSPLs. Amino acid residues that are highly conserved in different sequences are marked with a blue background and an exclamation mark below; amino acid residues that are similar in different sequences are marked with a red background and an asterisk below. LOGO is above the aligned sequence

Fig. 9

Regulatory network analysis. A Regulation of L-Phe biosynthesis by SbSPLs. B Regulation of lignin biosynthesis by SbSPLs. C Regulation of JA biosynthesis by SbSPLs. The red and blue lines represent positive and negative correlations, respectively. In the heatmap next to the gene name, red and blue represent higher and lower expression levels, respectively