Genome-Wide Identification and Functional Exploration of SBP-Box Gene Family in Black Pepper (Piper nigrum L.).

Jing Li,Xunzhi Ji,Baoduo Wu,Rui Fan,Chaoyun Hao

doi:10.3390/genes12111740

Jing Li, Xunzhi Ji + Show 3 more

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https://doi.org/10.3390/genes12111740

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Abstract

Black pepper (Piper nigrum L.), is dubbed “the King of Spices”. However, the lack of genic knowledge has limited the understanding of its physiological processes and hindered the development of its molecular breeding. The SBP-box gene family is an important family in plant development and integrates multiple physiological processes. Here, we made a genome-wide identification of the pepper SBP-box gene family to provide evolutionary and functional information about this conserved transcription factor. In total, 34 SBP genes were identified in pepper. All these pepper SBP genes were clustered into eight groups, and one pepper group was not found in Arabidopsis thaliana. Segment duplications played the most important role in the expansion process of pepper SBP genes, and all these duplications were subjected to purifying selection. Half of pepper SBP genes were found miR156 target sites, and 17 miR156s were predicted. The tissue expression analysis revealed the differential expression of pepper SBP genes. Eleven SBP genes were found in four co-expression networks, and the GO enrichment further provides a functional prediction for pepper SBP genes. This study lays a foundation for further studies of pepper and provides a valuable reference for functional mining of pepper SBP genes.

Highlights

Transcription factors (TFs), which are proteins that regulate gene expression by activating or repressing the transcription of downstream target genes, play essential roles in the regulatory networks of many development processes in all living organisms [1,2].Different families or subfamilies of TFs were found in plants according to their structure of DNA-binding domain, such as WRKY, MYB, MADS-box, DOF, and NAC transcription factor families
A. thaliana group was missing in pepper and one group was pepper specific
Compared with A. thaliana, significant gene expansion was found in some groups, resulting in a large number of redundant genes in these groups

Summary

Introduction

Transcription factors (TFs), which are proteins that regulate gene expression by activating or repressing the transcription of downstream target genes, play essential roles in the regulatory networks of many development processes in all living organisms [1,2].Different families or subfamilies of TFs were found in plants according to their structure of DNA-binding domain, such as WRKY, MYB, MADS-box, DOF, and NAC transcription factor families. Transcription factors (TFs), which are proteins that regulate gene expression by activating or repressing the transcription of downstream target genes, play essential roles in the regulatory networks of many development processes in all living organisms [1,2]. SBP genes were first found in Antirrhonum majus to regulate the expression of some MADS-box genes that play a critical role in floral development [3]. The SBP-box gene family play important roles in plant growth and development of the regulation network, and it is a key link to explore the molecular mechanism of plant growth and development [8]. The evolutionary patterns of the SBPbox gene family are highly consistent with the evolution of angiosperms, so it is an important resource to reveal the plant lineage-specific evolution process

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