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Tabugo, Sharon Rose M. » Research » Scholarly articles

Title	Course Outcome-based Students Research Experience (CORE): Primer Design and DNA Mini-barcoding of Seahorses for Wildlife Forensics and Conservation
Authors	Sharon Rose Tabugo
Conference	31st International Conference on Conservation Biology 2023 (ICCB 2023)
Abstract	Designing primers out of non-model organisms (seahorses) will be a good research experience that comes with an output product that can be useful for downstream and real-life applications such as wildlife forensics and conservation. For this research experience, custom primers were designed for seahorses to aid wildlife forensics and conservation. Primers were tested in silico, synthesized, and further tested for downstream applications such as Polymerase Chain Reaction (PCR), Gel Electrophoresis and sequencing. This study created a pipeline for designing mini-barcode primers using accessible software and integrative bioinformatic tools. Cytochrome b gene sequences containing highly variable and conserved genetic information served as a template for designing mini-barcode primers to optimize molecular identification of low-quality seahorse samples (frozen and dried). The four top-scoring novel mini-barcode primer sets based on oligos assessment were optimized through annealing. Five dried Hippocampus spp. (seahorse) samples and four frozen Hippocampus spp. samples were tested. PCR amplification and gel electrophoresis results revealed that all mini-barcode primers generated can amplify high-quality PCR products. Moreover, the base-calling of the trace files showed high-quality scores with 100% identity match based on BLAST identification. The novel mini-barcode primers generated will improve species identification of seahorse species. This process can be implemented for future student research experience since it proved highly feasible using readily online accessible tools and a basic molecular workbench.
Index terms / Keywords	primers, conservation, seahorses, molecular
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