Bioinformatics analysis of heat-shock proteins in pistachio compared to six other plant species

Heat-shock proteins (HSPs) are ATP-dependent chaperones conserved from bacteria to eukaryotes. In plants, they are necessary to control their normal growth, development, and immune responses to environmental stimuli. The present study aimed to comprehensively analyze the HSP gene family in pistachio and six other plants.

An alignment sequence of full-length proteins of Arabidopsis, pistachio, orange, corn, date, pine, and pea was prepared using MUSCLE and saved in the ClustalW format. Their phylogenetic analysis was conducted using the MEGA 6.0 program, with 1000 bootstrap replications. An unrooted Maximum-Likelihood was established by the Jones-Taylor-Thornton (JTT) model and the same alignment file. Conserved motifs in putative protein sequences were recognized by the MEME program using default parameters. In order to predict the structure of proteins, the phyre2 web server was used.

According to the sequence alignment, conserved amino acid sequences showed that pistachio and pea shared the greatest similarity. Besides, pistachio and orange showed the least identity. The phylogenetic tree revealed that within the same sub-families, the most closely related StHsp70 members assigned similar exon/intron structures and intron numbers. Additionally, 18 putative conserved motifs were identified.

The present survey indicated the functional characteristics of the HSP genes and provided basic information on pistachio and other plants with a high commercial and economic value for further studies on their biological functions.