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Identification, molecular characterization, and expression analysis of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family in Betula platyphylla Suk.

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Abstract

Key message

20 SPL genes were identified in Betula platyphylla Suk., and their sequence features and expression profiles provide useful information for further studies on their function.

Abstract

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL), a family of plant-specific transcription factors, plays a vital regulatory role in plant growth and development. However, information on SPL genes is largely undefined in Betula platyphylla Suk., an economically important tree species in China. Twenty full-length open read frames of SPL genes in B. platyphylla were identified and designated BplSPL1 to BplSPL20. Phylogenetic analyses showed that the genes were divided into eight groups. In addition, 12 BplSPL genes were suggested to be putative targets of miR156. Tissue-specific expression analysis of BplSPL genes indicated diverse spatiotemporal expression patterns. Most BplSPL genes had high transcription levels in leaves, female inflorescences, and male inflorescences. BplSPLs showed significant differences in male development, indicating that these genes may play different roles in this development process. Most miR156-targeted BplSPLs genes were gradually downregulated as female development progressed, whereas the expression levels of miR156 increased during female inflorescence development. This indicated that the miR156/SPL module plays an important role in female development. We also discussed the possible roles that BplSPL genes may play in leaves. Taken as a whole, these results provide a molecular basis for the further functional study of SPL genes in B. platyphylla and are a supplement to the systematic analysis of SPL genes in forest tree species.

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Abbreviations

SPL:

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE

NLS:

Nuclear localization signal

MW:

Molecular weight

NM:

Normal male inflorescences

F:

Female inflorescences

MM:

Mutant male inflorescences

MFE:

Minimal folding free energy

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Acknowledgements

We thank Yan Zhang and Minxiao Guan for providing the transcriptome data. We are also grateful to Ruihai Chai and Prof. Chenghao Li for critical reading and advice on the manuscript.

Funding

This work was supported by the Fundamental Research Funds for the Central Universities (2572015EA05), the Fundamental Research Funds for the Central Universities (2572017AA01) and the National Natural Science Foundation of China (J1210053).

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Authors and Affiliations

  1. College of Life Science, Northeast Forestry University, Harbin, 150040, China

    Xiaoqing Hu, Chuang Liu, Jing Tian, Yong Zhang, Qiqi Xin, Aihua Chen, Dou Li & Xuemei Liu

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  1. Xiaoqing Hu
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  2. Chuang Liu
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Correspondence to Xuemei Liu.

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Fig. S1

Characteristics of predicted proteins of BplSPLs compared to AtSPLs and PtSPLs (EPS 623 kb)

Fig. S2

Multiple sequence alignments and sequence logos for the SBP domains of BplSPL genes. The two zinc fingers (Zn-1/2) and a nuclear localization signal (NLS) are shown. Multiple sequence alignment was performed using BioEdit. Sequence logos were obtained from Weblogo online software. Red boxes indicate the conserved sites of zinc fingers (EPS 1811 kb)

Fig. S3

Alignment of complete BplSPL peptides. The DNA-binding domain is boxed, and acidic amino acids in the N-termini are marked by red triangles (PDF 4613 kb)

Fig. S4

Motif compositions of B. platyphylla SPL genes. Schematic representation of the conserved motifs as predicted using MEME, with groupings based on the phylogenetic tree. Each colored box with a number represents a conserved motif. Box size indicates motif length (EPS 1216 kb)

Fig. S5

Sequence alignment of corrected BplSPL sequences obtained by cloning and the corresponding sequences from the transcriptome data (PDF 10328 kb)

Fig. S6

The secondary structures of miR156 precursors in B. platyphylla. miR156 mature sequences are shown in red (EPS 1106 kb)

Fig. S7

Sequence alignment of BplmiR156 complementary sequences within the BplSPL genes. BplSPL gene names in black indicate that the miR156 binding sites are in their coding regions; names in red indicate genes with miR156 binding sites in their 3′UTRs (EPS 696 kb)

Table S1

Sequences of primers used for cloning (XLSX 9 kb)

Table S2

Sequences of primers used for qRT-PCR (XLSX 10 kb)

Table S3

Differentially expressed BplSPLs among the three types of inflorescences based on transcriptome analysis (XLSX 11 kb)

Table S4

PtSPL and AtSPL gene names and basic information (XLSX 11 kb)

Table S5

Consensus sequences of 15 motifs identified in the BplSPLs (DOC 38 kb)

Table S6

Mature sequences and precursors of miR156 in B. platyphylla (DOCX 14 kb)

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Hu, X., Liu, C., Tian, J. et al. Identification, molecular characterization, and expression analysis of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family in Betula platyphylla Suk.. Trees 34, 229–241 (2020). https://doi.org/10.1007/s00468-019-01913-7

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