Identification and characterization of some snakin gene family members in onion (Allium cepa L.)

Antimicrobial peptides (AMPs) are one of the most important defense barriers of plants against a wide range of pathogens. The snakins attract special attention because they are one of the most important and main cysteine-rich peptides among plant anti-microbial peptides. In the present study, some snakin gene family members were identified and characterized from onion (Allium cepa L.) using bioinformatics and experimental methods. All snakin protein sequences were retrieved from NCBI database. The snakin consensus sequence was obtained from alignment of retrieved sequences. Then, the consensus sequence was aligned against the onion transcriptome using tBLASTn tool. The resulting sequences were analyzed to determine the full-ORF, and to prediction of functional domains, signal peptides, subcellular localization, physicochemical properties, amino acid frequency and anti-microbial activity. The complete coding sequence of snakin genes were amplified by PCR. Finally, the presence of seven snakin genes, with an average ORF length of 332 bp, were confirmed in onion. The high similarity of the onion snakin genes with homologous snakin genes belonging to other plant species in terms of nucleotide and protein sequences as well as structural was revealed by bioinformatics analysis. The results also showed that all identified onion snakins had the potential antimicrobial activity. Due to the potential antimicrobial activity of identified peptides, by producing these peptides in different expression systems, they can be used as new antimicrobial agents against human, animal and plant pathogens.