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Genomic organization, phylogenetic comparison, and expression profiles of the SPL family genes and their regulation in soybean

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Abstract

SQUAMOSA Promoter-Binding Protein-Like (SPL) genes form a major family of plant-specific transcription factors and play an important role in plant growth and development. In this study, we report the identification of 41 SPL genes (GmSPLs) in the soybean genome. Phylogenetic analysis revealed that these genes were divided into five groups (groups 1–5). Further, exon/intron structure and motif composition revealed that the GmSPL genes are conserved within their same group. The N-terminal zinc finger 1 (Zn1) of the SBP domain was a CCCH (Cys3His1) and the C terminus zinc finger 2 (Zn2) was a CCHC (Cys2HisCys) type. The 41 GmSPL genes were distributed unevenly on 17 of the 20 chromosomes, with tandem and segmental duplication events. We found that segmental duplication has made an important contribution to soybean SPL gene family expansion. The Ka/Ks ratios revealed that the duplicated GmSPL genes evolved under the effect of purifying selection. In addition, 17 of the 41 GmSPLs were found as targets of miR156; these might be involved in their posttranscriptional regulation through miR156. Importantly, RLM-RACE analysis confirmed the GmmiR156-mediated cleavage of GmSPL2a transcript in 2–4 mm stage of soybean seed. Alternative splicing events in 9 GmSPLs were detected which produces transcripts and proteins of different lengths that may modulate protein signaling, binding, localization, stability, and other properties. Expression analysis of the soybean SPL genes in various tissues and different developmental stages of seed suggested distinct spatiotemporal patterns. Differences in the expression patterns of miR156-targeted and miR156-non-targeted soybean SPL genes suggest that miR156 plays key functions in soybean development. Our results provide an important foundation for further uncovering the crucial roles of GmSPLs in the development of soybean and other biological processes.

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Acknowledgements

This work was funded by the Department of Biotechnology (DBT), India.

Author contributions

RK AD conceived and designed the experiments. RK RG performed the experiments. RK RG analyzed the data. RK SK AD wrote the paper.

Author information

Authors and Affiliations

  1. Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India

    Rajiv K. Tripathi, Sweta Kumari & Anil Dahuja

  2. Department of Plant Science, McGill University, 21111 Rue Lakeshore, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada

    Rajiv K. Tripathi

  3. Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, India

    Ridhi Goel

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  1. Rajiv K. Tripathi
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Correspondence to Rajiv K. Tripathi.

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Communicated by Sureshkumar Balasubramanian

Electronic supplementary material

Fig. S1

Motif sequences in soybean SPL proteins. Conserved motifs in the SPL proteins of soybean elucidated using online MEME tool. Each motif is represented by a number in the colored box (GIF 16 kb)

High-resolution image (TIFF 517 kb)

Fig. S2

The miR156 members and their targets in soybean. The gray bar represents the transcript of SPL genes with the positions of the SBP domain indicated by black bars and the miR156 targeting site indicated by a red bar (GIF 8 kb)

High-resolution image (TIFF 296 kb)

Table S1

List of soybean SPL genes identified in this study (XLSX 12 kb)

Table S2

Genomic sequence of soybean SPL genes (TXT 206 kb)

Table S3

Coding sequence (CDS) of soybean SPL genes (TXT 53 kb)

Table S4

Protein sequence of soybean SPL genes (TXT 18 kb)

Table S5

SBP domain sequence of all 169 SPL proteins (TXT 14 kb)

Table S6

Summary of GmSPL genes duplication events (XLSX 14 kb)

Table S7

Summary of GmSPL transcript variants produced from alternative splicing (XLSX 11 kb)

Table S8

Details of miR156 targets in GmSPL transcript variants (XLSX 24 kb)

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Tripathi, R.K., Goel, R., Kumari, S. et al. Genomic organization, phylogenetic comparison, and expression profiles of the SPL family genes and their regulation in soybean. Dev Genes Evol 227, 101–119 (2017). https://doi.org/10.1007/s00427-017-0574-7

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