SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer.

Shaokun Li,Lei Zhu,Yanfang Wang,Yingjie Su,Yi Wang,Kangyu Wang,Yang Jiang,Li Li,Yue Jiang,Jun Wu,Meiping Zhang,Honghua Sun,Mingzhu Zhao

doi:10.3390/plants9030354

Abstract

SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identification, evolutionary analysis, structure analysis, and expression characteristics analysis of SPL gene family in Panax ginseng by bioinformatics. We annotated the PgSPL gene family and found that they might involve in multiple functions including encoding structural proteins, but the main function were still focused on the binding function. The result showed that 106 PgSPL transcripts were classified into two clades - A and B, both of which respectively consisted of three groups. Besides, we profiled PgSPL transcripts’ genotypic, temporal, and spatial expression characteristics. Furthermore, we calculated the correlation of PgSPL transcripts in the 14 tissues of a 4 years old ginseng and 42 farmers’ cultivars farmers’ cultivars of 4 years old ginsengs’ roots with both results showing that SPL transcripts formed a single network, which indicated that PgSPLs inter-coordinated when performing their functions. What’s more, we found that most PgSPL transcripts tended to express in older ginseng instead of younger ginseng, which was not only reflected in the expression of more types of SPL transcripts in older ginseng, but also in the higher expression of SPL transcripts in older ginseng. Additionally, we found that four PgSPL transcripts were only massively expressed in roots. According to PgSPL transcripts’ expression characteristics, we found that PgSPL23-35 and PgSPL24-09 were most proper two transcripts to further study as ginseng age’s molecular marker. These results provide the basis for further elucidation of the PgSPL transcripts’ biological function in ginseng and ginseng genetics improvement and gene breeding in the future.

Highlights

Transcription factors (TFs) are a group of protein that can bind to the sequence upstream of a gene to regulate the spatial or temporal expression of it [1]
Taking the SQUAMOSA promoter binding proteins (SBPs) domain (Pfam:PF03110) as query, we obtained 478 transcripts; taking as queries the nucleotide sequence of SQUAMOSA promoter binding protein-like (SPL) transcripts in other species, we obtained 209 transcripts; taking as query the SBP amino acid sequence downloaded from Plant Transcription Factor Database, we obtained 30,992 transcripts
The sequences identified as including SBP were rechristened PgSPL01-PgSPL30 (Table S1), and transcripts of the same gene were distinguished by digital suffixes (e.g., −01)

Summary

Introduction

Transcription factors (TFs) are a group of protein that can bind to the sequence upstream of a gene to regulate the spatial or temporal expression of it [1]. SQUAMOSA promoter binding protein-like (SPL) gene family is a kind of TFs that encode the SQUAMOSA promoter binding proteins (SBPs). It was first identified in Antirrhinum majus with the function of regulating MADS-box genes in the early stage of flower development [2]. Through the findings of these study, the SPL gene family has multiple biological functions in plant growth and development including flowering time [8,9], sporocytes formation [10] and leaf initiation [11,12]. The SPL genes act as the target of miR156 that controlling the phase transitions between vegetative and reproductive, which is critical to plant reproductive success [13]

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Discussion

Conclusion