Species-Specific qPCR Detection Reveals Offshore Distribution of Gonyaulax polygramma (Dinophyceae) in Korean Coastal Waters

Gonyaulax polygramma is a bloom-forming dinoflagellate that can be difficult to identify accurately during routine harmful algal bloom (HAB) monitoring, particularly when morphologically similar Gonyaulax species occur together in field samples. To improve species discrimination and quantitative detection, we developed a species-specific TaqMan qPCR assay targeting the 28S rDNA region of G. polygramma and applied it to field samples collected during a four-year survey in Korean coastal waters. The developed primer–probe set showed high specificity without cross-reactivity with tested non-target microalgae. The assay exhibited high linearity (R2 = 0.999), amplification efficiencies of 92.01–99.36%, and a detection limit of 10 copies reaction−1. Field application revealed clear regional differences in distribution patterns. G. polygramma was rarely detected in the semi-enclosed Jinhae Bay, whereas relatively high abundances were observed at offshore-influenced stations in the Tongyeong–Yeosu–Wando region during summer. These results suggest that G. polygramma occurs locally in offshore-influenced coastal waters rather than being uniformly distributed along the southern coast of Korea. The developed qPCR assay provides a reliable molecular tool for detecting G. polygramma and can complement morphology-based monitoring of Gonyaulax species in coastal HAB surveillance programs.