In silico characterization, evolutionary analysis, and structural modeling of HSP70 gene family in carrot (Daucus Carota L.)

Abstract

Heat-shock protein 70 (HSP70) chaperones play indispensable roles in protein folding, homeostasis, and protecting plants against abiotic stress. While well-characterized in model species, a comprehensive genome-wide analysis of the HSP70 family in carrot (Daucus carota L.) has been lacking. The study aimed to identify the DCHSP70 gene family members in the Daucus carota genome and elucidate their evolutionary relationships, structural characteristics, and potential functional roles under stress conditions. We performed a systematic genome-wide analysis using bioinformatic approaches to identify family members. Phylogenetic relationships were analyzed using neighbor-joining methods, while chromosomal distribution and synteny were visualized to track evolutionary analysis. Promoter regions were screened for cis-regulatory elements, and protein-protein interaction (PPI) networks were constructed. Additionally, 3D structural modeling was performed using SWISS-MODEL and I-TASSER servers. A total of 52 DCHSP70 genes were identified and classified into six distinct phylogenetic subgroups based on their homology with Arabidopsis thaliana and Solanum lycopersicum. Chromosomal mapping revealed an uneven distribution across the nine chromosomes. Synteny analysis indicated that segmental duplication was the primary driving force behind the family evolution, with all the paralogous pairs undergoing strong purifying selection (Ka/Ks < 1). Analysis of cis-regulatory elements in the promoter regions identified a predominance of light, hormone, and stress-responsive motifs (e.g., ABRE, LTR, MBS), suggesting a complex regulatory network for environmental adaptation. The PPI network analysis revealed highly significant connectivity (p < 1.0e-16), with functional enrichment in protein refolding and cellular stress response. Structural modelling confirmed that most DCHSP70 proteins are conserved as monomers, with reliable 3D structures predicted even for divergent members like DCHSP70-15 and DCHSP70-46 using threading-based approaches. This study provides the first systematic characterization of the DCHSP70 family in carrot. The finding highlights the evolutionary conservation of these genes and their crucial role in the plant’s stress response mechanism, providing valuable targets for future breeding programs aimed at improving stress tolerance in Daucus carota.