Genetic Variation and DNA Metabarcoding Analyses of the Pacific Oyster Magallana gigas from Tongyeong and Gadeokdo in Korea

Abstract

The Pacific oyster, Magallana gigas, is one of the most important and valuable aquaculture species in South Korea. More researches about this species are necessary for designing optimal aquaculture management guidelines. In this study, M. gigas genetic variation from two aquaculture farms in Tongyeong and Gadeokdo was determined using the partial mitochondrial cytochrome c subunit I (COI) gene. The genetic diversity was slightly higher at Tongyeong (haplotype diversity, h = 0.5154 and nucleotide diversity, π = 0.000927) than at Gadeokdo (h = 0.4397 and π = 0.000689), but both populations were characterized by moderate haplotype diversity and low nucleotide diversity. The M. gigas haplotype networks between Tongyeong and Gadeokdo and among 12 populations (including Tongyeong and Gadeokdo) had the same star-like pattern, indicating close genealogical relationships among M. gigas populations. The analysis of molecular variance (AMOVA) revealed no genetic structure between the M. gigas populations. Besides, M. gigas diet composition and its variation from these two aquaculture farms were determined in four seasons using fecal DNA metabarcoding analysis. By targeting the 18S rDNA V9 regions of all eukaryote organisms, the next-generation sequencing sufficiently generated 2,579,120 sequences. The diversity and stability of M. gigas diet composition in Tongyeong were greater than those in Gadeokdo in four seasons with the highest in the fall and the lowest in the winter. Taxonomic compositions based on the frequency of ASV occurrence identified 14 phyla, 23 classes, 43 orders, 53 families, 56 genera, and 82 species. Among them, Dinoflagellata (dinoflagellates) and Bacillariophyta (diatoms) appeared as the two predominant phyla. High proportions of Arthropoda and Mollusca were found, indicating no selective feeding of M. gigas. Many M. gigas diet compositions were identified at the genus and species level, revealing several harmful dinoflagellates. There was a clusteriz of the M. gigas diet composition between Tongyeong and Gadeokdo according to seasons. The fundamental information in this study is useful and necessary for designing aquaculture management guidelines of M. gigas in South Korea.