Genome-Wide Identification and Analysis of the SBP-Box Family Genes under Phytophthora capsici Stress in Pepper (Capsicum annuum L.).

Huai-Xia Zhang,Bo-Ya Lu,Abid Khan,Zhen-Hui Gong,Jing-Hao Jin,Yu-Mei He,Wei-Guo Chai,Da-Wei Li

doi:10.3389/fpls.2016.00504

Abstract

SQUAMOSA promoter binding protein (SBP)-box genes encode plant-specific transcription factors that are extensively involved in many physiological and biochemical processes, including growth, development, and signal transduction. However, pepper (Capsicum annuum L.) SBP-box family genes have not been well characterized. We investigated SBP-box family genes in the pepper genome and characterized these genes across both compatible and incompatible strain of Phytophthora capsici, and also under different hormone treatments. The results indicated that total 15 members were identified and distributed on seven chromosomes of pepper. Phylogenetic analysis showed that SBP-box genes of pepper can be classified into six groups. In addition, duplication analysis within pepper genome, as well as between pepper and Arabidopsis genomes demonstrated that there are four pairs of homology of SBP-box genes in the pepper genome and 10 pairs between pepper and Arabidopsis genomes. Tissue-specific expression analysis of the CaSBP genes demonstrated their diverse spatiotemporal expression patterns. The expression profiles were similarly analyzed following exposure to P. capsici inoculation and hormone treatments. It was shown that nine of the CaSBP genes (CaSBP01, 02, 03, 04, 05, 06, 11, 12, and 13) exhibited a dramatic up-regulation after compatible HX-9 strain (P. capsici) inoculation, while CaSBP09 and CaSBP15 were down-regulated. In case of PC strain (P. capsici) infection six of the CaSBP genes (CaSBP02, 05, 06, 11, 12, and 13) were arose while CaSBP14 was down regulated. Furthermore, Salicylic acid, Methyl jasmonate and their biosynthesis inhibitors treatment indicated that some of the CaSBP genes are potentially involved in these hormone regulation pathways. This genome-wide identification, as well as characterization of evolutionary relationships and expression profiles of the pepper CaSBP genes, will help to improve pepper stress tolerance in the future.

Highlights

Transcription factors (TFs) are DNA-binding proteins that regulate gene expression at the level of mRNA transcription
The hidden Markov model (HMM) profile of the SQUAMOSA promoter binding protein (SBP) domain was used as a BLAST query against the pepper genome
A total of 15 and 16 candidate SBPbox genes were obtained from pepper cultivars CM334 and Zunla-1, respectively

Summary

Introduction

Transcription factors (TFs) are DNA-binding proteins that regulate gene expression at the level of mRNA transcription. SQUAMOSA promoter binding protein (SBP)box genes encode a TFs that contain a highly conserved DNAbinding domain termed the SBP domain (Klein et al, 1996; Cardon et al, 1999). This domain comprises approximately 76 amino acid residues that are involved in both DNA binding and nuclear localization, including two zinc-binding sites (Yamasaki et al, 2004). Additional SBP-box genes were later identified, isolated, and characterized in many plants, including Arabidopsis thaliana (Cardon et al, 1999), silver birch (Lannenpaa et al, 2004), Salvia miltiorrhiza (Zhang et al, 2014), rice (Xie et al, 2006), maize (Chuck et al, 2010), tomato (Salinas et al, 2012), grape ( Hou et al, 2013b), and Gossypium hirsutum (Zhang et al, 2015)

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Results

Conclusion