Evaluation of the applicability of 28S rRNA and COI genes in the molecular identification of planktonic copepods from the Northwest Pacific

Copepods are a crucial component of marine ecosystems, serving as a primary food source for numerous marine species and playing a significant role in aquatic food webs. Traditional morphological identification methods are often challenging due to the small size and subtle morphological differences among species. Molecular identification techniques have emerged as powerful tools for species discrimination. This study evaluates the effectiveness of the nuclear 28S ribosomal RNA (28S rRNA) and mitochondrial cytochrome c oxidase I (COI) genes in identifying copepod species from the Northwest Pacific. Zooplankton samples were collected using vertical net tows from 32 stations across an area of 1,320,000 km 2 in the Northwest Pacific. We analyzed sequences and conducted phylogenetic analyses on planktonic copepods. We obtained 110 valid 28S rRNA sequences from 45 species, representing 2 orders, 15 families, and 29 genera, and 62 valid COI sequences from 30 species. Notably, this study provides the first 28S rRNA and COI sequence data for Euchaeta tenuis , Euchirella indica and Scolecithricella vittata. Our findings indicate that the average interspecific genetic distances for 28S rRNA and COI are approximately 93.0 and 53.0 times higher, respectively, than the average intraspecific genetic distances, meeting the requirements for DNA barcoding. While COI-based barcodes exhibited distinct barcode gaps, 28S rRNA showed a 7 % overlap between intra- and interspecific genetic distances; however, Jeffries-Matusita (J-M) statistical test confirmed a significant gap for 28S rRNA. Compared to COI, 28S rRNA is more effective in delineating genera and higher taxonomic levels such as families revealed by phylogenetic analyses. Additionally, 28S rRNA demonstrated higher amplification success rates and comparable species-level identification performance to COI. • First study to obtain COI and 28S rRNA sequences for three species . • 28S rRNA gene is effective for genus and family-level phylogenetic analysis of copepods. • COI gene excels at species and intra-species identification in copepods.