Identification and characterization analysis of Ascorbate Peroxidase (APX) and Glutathione Peroxidase (GPX) Gene families in rapeseed (Brassica napus L.)

Background and Aim: Ascorbate peroxidase is one of the most important antioxidants that breaks down the peroxidase into water and oxygen molecules. Ascorbate peroxidase plays an important role in stomatal activity by regulating the concentration of hydrogen peroxide in the cells of stressed plants. Glutathione peroxidases belong to the non-hemi thiol peroxidase family. Glutathione peroxidase enzyme uses glutathione to reduce peroxides to alcohol and prevent the formation of free radicals. In previous studies of these two genes in different plants, using bioinformatics methods, for apx gene family in Arabidopsis thaliana ۸ gene, Oryza sativa ۶ gene, Solanum Lycopersicum ۷ gene, Zea mays ۸ genes and Vitis vinifera ۶ genes were identified. For gpx gene family in Arabidopsis thaliana ۸ gene, Oryza sativa ۵ gene, Solanum Lycopersicum ۵ gene, Zea mays ۳ genes and Vitis vinifera ۵ gene was identified. This study aimed to systematically identify and determine the structural, functional and phylogenetic characteristics of apx and gpx gene families in canola by bioinformatics.Methods: Protein sequences of apx and gpx families in mentioned plants were used as primary sequences by the Blastp method to identify homologous proteins in the rapeseed genomic database. After receiving all sequences, duplicate sequences were deleted. General properties of apx and gpx proteins such as molecular weight, isoelectric point, number, and amino acid types were obtained from the Expasy site. Protein alignment was first performed using ClestelW software and subsequent editing was performed and then MEGA software was used to plot the phylogenetic tree. The accuracy of the plotted tree was evaluated through Bootstrap. Finally, the number of genes in each family was determined.Results: Following the steps described above, in the rapeseed genome, thirty genes were found for the gpx gene family and ۱۳۷ genes for the apx gene family. After drawing the primary phylogenetic tree, some of the genes found were deleted using homology and Bootstrap comparisons. Finally, twenty-eight genes were selected for gpx and twenty-five genes for apx. The final phylogenetic tree was then plotted.Conclusion: Because of the larger number of rapeseed chromosomes than the previous plants studied, the number of genes in these two gene families can be explained more than the previous plants. The deletion of some of the genes obtained due to low Bootstrap and low homology with the genes of other plants can also be explained. However, further molecular and physiological studies are needed to accurately quantify the genes of these two gene families to confirm the evidence obtained through bioinformatics.

Keywords:

Antioxidant enzymes , Bioinformatics , Gene family , Reactive oxygen species