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

Abstract

Background and Objective: In plants, the 70 kDa heat shock proteins (Hsp70-s) play important roles during growth and development and in response to stresses. This study aimed to provide comprehensive information on the Hsp70 family in cocoa (Theobroma cacao), one of the most important tropical perennial cash crops worldwide. Materials and Methods: A basic local alignment search tool (TBLASTN) against the cocoa genome was performed using Arabidopsis Hsp70-s as queries to detect TcHsp70-s. Sequence analyses were carried out by various bioinformatics tools. Results: A total of 18 members of the Hsp70 family has been detected and characterized in the cocoa genome. All general properties, such as physic-chemical parameters, gene structure, phylogenetic tree and sub-cellular localization, were determined using a variety of bioinformatics tools. The expression patterns of the TcHsp70 genes in different stages of the zygotic and somatic embryos were investigated. In addition, expression profiles of the TcHsp70 genes under Phytophthora megakarya inoculation were analyzed. Conclusion: The results of this study revealed the features and expression analyses of Hsp70 genes in cocoa. These findings could provide a strong foundation for further research of the TcHsp70 family, which could aid in the development and stress tolerance of cocoa species.

Genome-wide identification, characterization, and expression analysis of the small auxin-up RNA gene family during zygotic and somatic embryo maturation of the cacao tree (Theobroma cacao)

“…The full-length amino acid sequences of SAUR proteins in cacao were used as seed sequences for a search in the Expasy Protparam [31,32] as previously guided [9,[33][34][35][36]. Particularly, the SAUR protein's common features, including protein length, isoelectric point (pI), molecular weight (mW), aliphatic index (AI), and grand average of hydropathicity (GRAVY) were estimated.…”

“…The full-length amino acid sequences of SAUR proteins in cacao were used to generate an unrooted phylogenetic tree as previously guided [9,[33][34][35][36]. Firstly, the ClustalW software [37,38] was used for the multisequence alignment of the SAUR proteins in cassava.…”

“…The duplicated events that occurred in the SAUR gene family in cacao were predicted based on the MEGAbased phylogenetic tree as previously described [9,[33][34][35][36]. Particularly, SAUR members in the same clade with high bootstrap values were assigned as duplicated pair.…”

“…To address the issues caused by adverse environmental conditions, various studies have concentrated on the functions of gene families [7][8][9][10], because understanding the roles of these functional and regulatory genes may open up the possibility of developing new climate change-adapted lines through genetic engineering. Of our interest, the small auxin-up RNA (SAUR) proteins serve as the largest sub-group of the expansive auxin response factor gene family in higher plant species.…”

“…Gene exon-intron structure characteristics of genes encoding the SAUR proteins in cacao were analyzed as previously guided [9,[33][34][35][36]. Specifically, the genomic DNA sequence and coding DNA sequence of each gene encoding SAUR protein in cacao were used to align in the Gene Structure Display Server [43].…”