Genome-Wide Identification and Expression Analysis of Hsf and Hsp Gene Families in Cucumber (Cucumis Sativus L.)

Abstract

Heat shock proteins (Hsps) are molecular chaperones that participate in plants' response to environmental stresses, including heat stress, and also play an essential role in plant growth and development. Hsps expression is monitored and regulated by specific types of transcription factors known as heat shock factors (Hsfs). Although the role of Hsfs and Hsps in stress response has been investigated in some plants, their role is still poorly understood in cucumber (Cucumis sativus L.). To reveal the mechanisms of cucumber Hsf and Hsp coping with various stresses, the analyses of cucumber Hsf and Hsp gene families were conducted using bioinformatics-based methods. A total of 23 Hsfs and 72 Hsps were identified in the cucumber genome (v3.0), and the gene structure and motif composition are relatively conserved in each subfamily. At least 23 pairs of heat shock genes underwent gene duplication in cucumber. A cis-element analysis is implicit that CsHsfs and CsHsps possessed at least one hormone or stress response cis-element, suggesting that CsHsf and CsHsp genes could respond to different stress conditions. Heatmaps of the CsHsf and CsHsp gene families indicated that most heat shock genes were expressed in different tissues and organs. RNA-seq showed that most of the cucumber Hsf and Hsp genes are differentially expressed upon exposure to biotic and abiotic stresses. These results provide valuable information to clarify the evolutionary relationship between the CsHsf and CsHsp family and to facilitate the functional characterization of the CsHsf and CsHsp genes in future studies.

Genome‐wide identification and expression analysis of heat shock protein gene family in cassava

“…Similar findings have been confirmed in many other species (X. Chen et al, 2021;Ke et al, 2022). Synteny analysis revealed the presence of syntenic Hsp genes in Arabidopsis, rice, yam, P. trichocarpa, and rubber tree.…”

“…Concurrently, BLASTp was performed with an E-value <10 −2 using the Hsp protein sequences from Arabidopsis as query sequences (X. Chen et al, 2021;Ding et al, 2017). These results were merged, and their amino acid sequences were submitted to the CDD (https:// www.ncbi.nlm.nih.gov/cdd) and Pfam databases (manual verification of the complete Hsp domain).…”

“…Understanding cassava Hsps holds the potential to provide practical approaches for the genetic improvement of cassava. Heat shock proteins have been extensively characterized in many species, with 153 Hsps characterized in Arabidopsis (Arabidopsis thaliana), 72 Hsps in cucumber (Cucumis sativus), 753 Hsps in wheat (Triticum aestivum), and 283 Hsps in watermelon (Citrillus lanatus) (Altunoglu et al, 2019;X. Chen et al, 2021;A.…”

Genome-Wide Identification and Analysis of Heat Shock Protein 70 Family in Theobroma cacao

“…Genome-wide identification of the Hsp70 family was done for many species such as A. thaliana 19 , rice (O. sativa) 20 , poplar (P. trichocarpa) 21 , soybean (G. max) 11 , potato (S. tuberosum) 22 , tea (C. sinensis) 23 , cabbage (B. oleracea var. capitata) 18 , cucumber (C. sativus L.) 24 and A. sinensis 25 . In accordance with the literature, a genomic survey of Hsp70 in these plants was re-performed (Table 2).…”

“…To date, the Hsp70 family has been identified and characterized in numerous higher plant species, such as Arabidopsis thaliana (18 genes) 19 , rice (Oryza sativa) (32 genes) 20 , poplar (Populus trichocarpa) (20 genes) 21 , soybean (Glycine max) (61 genes) 11 , potato (Solanum tuberosum) (20 genes) 22 , tea plant (Camellia sinensis) (18 genes) 23 , cabbage (Brassica oleracea var. capitata) (52 genes) 18 , cucumber (Cucumis sativus L.) (12 genes) 24 and Aquilaria sinensis (15 genes) 25 . However, the knowledge of the Hsp70 family in cocoa has been still unavailable.…”