Bioinformatics characterization of heat shock protein and heat shock factor genes in zucchini and expression profiles in different abiotic stress conditions

Heat shock proteins (Hsps) are involved in response mechanism of the environmental stress by providing protein homeostasis as well as the normal growth and development processes of the plant. Heat shock response in plants is regulated by heat shock transcription factors (Hsfs) activating the expression of Hsps. The Cucurbitaceae family includes many plants with economic and nutritional value such as cucumber, melon, watermelon and pumpkin. Cucurbita pepo (zucchini), which is produced throughout the year in our country, is another member of this family that has economic value. Seyden F1 and Cordelia F1 are the two most preferred zucchini varieties in the domestic market and export. In this study, a total of 464 Hsp genes, including 44 CpsHsp, 188 CpHsp40, 42 CpHsp60, 28 CpHsp70, 10 CpHsp90, 152 CpHsp100 family members and 77 CpHsf genes in zucchini genome have been identified in silico. The characteristic features of the identified genes and proteins were revealed by chromosomal location, exon-intron and motif organization, intra-familial phylogenetic relationships, orthologous relationships, miRNA and protein-protein interactions, duplication events, estimated three-dimensional structures, gene ontology analyses. Based on the heatmaps created using the stress-related transcriptome data in the literature, genes with significant changes in expression were determined for each gene family. In the molecular part of the study, the expression profiles of these genes under high temperature, drought and high temperature- drought combined stresses were evaluated by qRT-PCR for Seyden F1 and Cordelia F1 cultivars. It has been observed that both varieties respond to stress by mostly increasing the expression levels of Hsp and Hsf genes. It indicates that Hsp70-20 and Hsf-68 genes, whose expression was increased in all time periods and under all stress conditions, play an active role in the stress tolerance mechanism of the plant. We believe that the Hsp and Hsf genes and proteins, which we have characterized with the omics approach, are valuable in terms of understanding the stress response mechanism of the zucchini. We anticipate that the marker genes and in silico interaction outputs determined in our study will contribute to crop improvement with cloning, advanced functional research and molecular breeding studies.