In Silico Genome-Wide Identification and Characterization of Glutathione Peroxidase Gene Family in Wild Cherries (Prunus avium L)

Biotic and abiotic stresses are the main problems affecting the quantity and quality losses of antioxidants in wild cherry (Prunus avium L), which provide health benefits to humans, such as anti-allergic, anti-inflammatory, antimicrobial, and anti-cancer benefits. Glutathione peroxidase (GPX) isoenzymes act a major role in responding to oxidative stresses through the multiple metabolic pathways. Protein sequences of GPXs family form Arabidopsis thaliana and Oryza sativa were used to identify homologous proteins by the BlastP in the sweet cherry’s genome. After the alignment, the existence of the specific domain, phylogenetic relationships, subcellular localization analysis, as well as exon-intron structures and conserved motives were evaluated in this study. MicroRNA target site and codon usage bias were also investigated. Furthermore, the existence of cis-regulatory element and SSR markers were identified. The three-dimensional structure of the GPXs protein prediction and the accuracy of the predicted model was also investigated. Regarding molecular docking, the best pose for considering the accuracy of binding site was evaluated. Finally, by analyzing biological process and molecular function, gene ontology of the predicted protein was considered. We identified the five GPX genes in P. avium that classified into ۳ separate groups based on their phylogenetic relationships. The predicted subcellular localization showed the GPX proteins that localized both chloroplast and mitochondria. Also, results showed ENC values were ranked ۴۵.۹۲ to ۵۹.۲۱ in PavGPX۳ and PavGPX۲. The results of cis‐regulatory elements showed PavGPX۸ contained ten cis‐regulatory elements which was the lowest number among PavGPXs. The best pose and protein interaction in the verified ۳D model were the first pose with the -۲۸.۵ minimization energy in docking process. It was concluded that the precise information on putative roles of P. avium GPXs genes could be helpful in determining their functional characterizations. The presence of several developmental process, stresses, light and hormones- responsive elements in the upstream of these genes, and GPXs‐targeted miRNAs suggested that GPX family members may play various roles in different biological responses. Finally, the GPXs gene was proposed as a good candidate for genetic engineering and breeding programs in order to introduce an abiotic stress- tolerant cultivar.

Keywords:

Abiotic stress , In silico analysis , Glutathione peroxidase , phylogenetic tree , Prunus avium L