Genome-wide identification and expression analysis of Hsf and Hsp gene families in cucumber (Cucumis sativus L.)

Xueqian Chen,Lina Wang,Zhiyuan Wang,Chunhua Chen,Rui Tang,Zhonghai Ren

doi:10.1007/s10725-021-00739-z

Abstract

Heat shock proteins (Hsps) are molecular chaperones that participate in plant growth and development, and in plant responses to environmental stresses, including heat stress, Hsps' expression is monitored and regulated by specific types of transcription factors known as heat shock factors (Hsfs). Although the roles of Hsfs and Hsps in stress response have been investigated in some plants, their roles are still poorly understood in cucumber (Cucumis sativus L.). To reveal the number of Hsfs and Hsps and their members coping with various stresses in cucumber, the comprehensive analyses of Hsf and Hsp gene families were conducted. A total of 23 Hsfs and 72 Hsps were identified in the cucumber genome (v3.0), and their gene structure and motif composition were found to be relatively conserved in each subfamily. At least 23 pairs of heat shock genes may have undergone duplication in cucumber. The cis-element analysis indicated that the promotors of CsHsfs and CsHsps possess at least one hormone or stress response cis-element, suggesting that CsHsf and CsHsp genes might respond to different stress conditions. RNA-seq showed that most CsHsf and CsHsp genes were sensitive to heat stress, but not all. Interestingly, CsHsf and CsHsp genes up-regulated by heat stress were also up-regulated by NaCl, indicating that cucumber shares common pathways in the responses to heat and salt stress. In addition, our results demonstrated that the fewer introns in the stress genes, the more sensitive they are, which leads to the stronger adaptability of plants to various developmental conditions and environmental stimuli. For instance, comparing with other Hsp families, the genes of CsHsp20 family are shorter in length and have fewer introns, and 39% of them are intronless, however, most of CsHsp20s were highly induced by heat stress. These results provide valuable information to further clarify the functional characterization of the CsHsf and CsHsp genes for plant breeding purposes.

Highlights

During growth and development, plants were exposed to a variety of strenuous stresses from the surrounding environment, including abiotic stresses such as high temperatures, drought, salinity, cold, and high light intensity and biotic stresses such as animal attack and pathogen invasion (Nejat and Mantri 2017)
Identification and analysis of heat shock factors (Hsfs) and Heat shock proteins (Hsps) genes in the cucumber genome After Hidden Markov Model (HMM) analysis, BLASTP and keyword search against the Cucumber Genomic Database (Version 3.0), a total of 23 Hsf and 72 Hsp genes in cucumber were identified, among which 33, 15, 12, 6 and 6 genes belonged to Hsp[20], Hsp[60], Hsp[70], Hsp[90] and Hsp[100] families, respectively
23 CsHsf and 72 CsHsp genes were unevenly distributed on 7 cucumber chromosomes, and the analysis showed that 10 CsHsf and 23 CsHsp genes were duplicated in the Cucumber genome, forming 13 segmentally duplicated gene pairs and 5 tandem duplicated gene groups (Fig. 4), indicating that both tandem and segmental duplications are conducive to the evolution of Hsf and Hsp genes in cucumber

Summary

Introduction

Plants were exposed to a variety of strenuous stresses from the surrounding environment, including abiotic stresses such as high temperatures, drought, salinity, cold, and high light intensity and biotic stresses such as animal attack and pathogen invasion (Nejat and Mantri 2017). To prevent the negative effects of high temperature on plants, such as water loss, growth reduction, photosynthesis efficiency reduction, some genes are sensitive to heat stress and can respond quickly (Xiong and Ishitani 2006). Heat shock factors (Hsfs), a specific type of transcription factor, normally exist as inactive proteins and can be induced rapidly to modulate growth responses under high temperature (Scharf et al 2012). Previous studies have shown that the protein structure of Hsfs is very conserved, in which the N-terminus was mainly composed of DNA-binding domain (DBD) and adjacent bipartite oligomerization domain (HRA/B or OD), and the C-terminal of Hsfs has nuclear localization signal (NLS), a nuclear output signal (NES) and activation peptide motif (AHA) (Guo et al 2016; Scharf et al 1990). According to the number of amino acid residues inserted between HR-A and HR-B, plant Hsfs can be divided into three main classes, namely: A, B, and C (Guo et al 2016)

Methods

Results

Discussion

Conclusion