Target-Specific Gene Sequence Search Strategy Using a Comparative Genomics Tool and Its Application to Food Testing

Target-specific gene detection for biological species identification is widely used in various food testing techniques, including the detection of genetically modified foods, and allergens and contaminants. These tests typically rely on unique genomic sequences of target species; however, the availability of gene markers is limited and no systematic method has been established for discovering new markers. In this study, we developed a workflow that combines OrthoFinder analysis with a newly developed BLAST+-based search system to comprehensively search for target-specific gene sequences (BLAST_TSN). We applied this workflow to three food types and successfully extracted target-specific sequences that effectively distinguished target species from nontargets, including closely related species within the same genus. The results demonstrate that this systematic workflow expanded the pool of available gene markers and can be applied to various food testing methods, including food inspection.