Agent-Specific Primer and Probe Design Using Bioinformatic Methods in Bacterial Fish Diseases

Abstract

The incidence of diseases in fishes grown in parallel with the development of aquaculture in our country is also increasing. Early isolation and identification of the disease is important for the treatment process. Bioinformatics software is invaluable in terms of both the specificity of the study design and the minimization of errors that can be faced, in order to construct a molecular-based work in the field of aquatic diseases.In this study, it is aimed to design the study by using specific Bioinformatic software and specific primer and probe in molecular based studies to be carried out with bacterial fish disease agents. For this purpose, Listonella (Vibrio) anguillarum sample which is effective in Listonellozis.In the results of working; On the genome with the accession number NCBI LK021130.1, the genes in the homology-low regions were screened. Probing experiments were carried out by selecting genes that contain the most appropriate specific sites for primer insertion. The vabS gene has been found to have the most appropriate sequence for this purpose. Specific areas for the primer on the vabS gene have been identified. The characteristics determined by bioinformatics software and primer design were obtained. Primer set and probe specificity were verified by testing in software databases. The 100% sequence of the obtained primer set was found to overlap only with L. anguillarum in all bacteria. The probe was tested in single-chain blast, confirming its specificity. PCR and electrophoresis steps were performed on the genome with the obtained primer set and probe.

Keywords: Fish diseases, Listonella anguillarum, Primer design, Bioinformatics, Probe design