Jong-Won Park

Triploid oysters are widely used in aquaculture, but their commercial species designation may not accurately represent their nuclear genomic composition, particularly when interspecific or polyploid broodstocks are involved. In this study, we combined whole-genome sequencing with a mitochondrial COI-based multiplex PCR assay to characterize commercial triploid Crassostrea gigas, C. angulata, and C. hongkongensis. Whole-genome allele-frequency analysis confirmed triploidy in all 15 individuals examined, comprising five individuals each from the A3N, G3N, and H3N groups. Cross-species ancestry dosage showed that G3N and H3N were predominantly assigned to their nominal species, whereas A3N exhibited mixed C. angulata–C. gigas nuclear ancestry, with approximately 2.2 and 0.7 haploid-equivalent copies assigned to these species, respectively. The minor C. hongkongensis assignment was interpreted as background cross-assignment rather than evidence of an additional ancestral contribution. Local-ancestry analysis further revealed chromosome-scale mosaics of zero, one, and two C. gigas-derived copies, with copy-weighted C. gigas contributions of approximately 0.69–0.88 haploid-equivalent copies among A3N individuals. This interspecific ancestry was supported by convergent evidence from complementary analyses of discrete dosage-state distributions, D-statistics with two alternative outgroups, and mapping-independent C. gigas-diagnostic 21-mers. All A3N individuals nevertheless carried C. angulata COI haplotypes, consistent with a C. angulata maternal lineage. The breeding history underlying the nuclear ancestry mosaics could not be resolved because the actual parental broodstock was unavailable for genomic analysis. A three-species multiplex PCR assay generated diagnostic products of 212, 359, and 169 bp for C. gigas, C. angulata, and C. hongkongensis, respectively, with no detectable cross-amplification at an optimized annealing temperature of 62 °C. Diagnostic amplification remained detectable with 1 ng of template DNA and was successfully applied to specimens from multiple Korean production sites and Dalian, China. These findings demonstrate complex nuclear ancestry in the five A3N individuals examined that was not captured by their nominal species designation or mitochondrial lineage alone. Although the observed ancestry proportions cannot be generalized to commercial A3N stocks as a whole, the results highlight the complementary roles of genome-wide ancestry analysis and rapid mitochondrial lineage authentication.

The Pacific oyster, Crassostrea gigas, is an important commercially farmed species in Korea. C. gigas exhibits low genetic diversity in wild populations in Korea. To address this, we bred Japanese broodstock for more than five generations and released them into two populations to increase genetic diversity. We also assessed whether this improvement was achieved by comparing them with a control population. In this study, we analyzed genetic diversity using 16 microsatellite loci of C. gigas. The observed heterozygosity H_O in the farmed population ranged up to 0.494, while in the wild population, it was 0.437. The farmed population had the highest genetic diversity, but the effective population size was low (105). The PD population size for resource creation was 403, which was higher than that of GH. The genetic structure was divided into two groups with K = 2. The first group consisted of the BR population, while the second group included the GH, GW, and PD populations. Therefore, we confirmed significant genetic differences between the farmed, wild, and resource creation populations. This study provides essential genetic information for future fishery resource development and conservation of C. gigas.

Numerous studies have explored alternative protein sources to fishmeal (FM) to enhance fish diets, yet limited research exists on their effects on maturation. This study assessed the impact of replacing FM with soy protein concentrate (SPC) supplemented with lysine and methionine on growth and gonadal development in olive flounder (Paralichthys olivaceus). Three diets were tested: a control (Con) diet with 60% FM and two diets replacing FM with 25% (LF1) and 50% (LF2) SPC. Fish were fed to apparent satiation twice daily for 12 months. Growth performance and feed intake were not significantly different between groups. However, the gonadosomatic index varied with diet. Muscle composition and amino acid levels were similar across treatments, though n-3 fatty acids were higher in Con. Spermatogonia was increased, and spermatogenesis was impaired in SPC groups. At 12 months, oocytes in Con diets had absorbed yolk globules, whereas this was absent in SPC groups. Growth-related genes in the brain (growth hormones and insulin-like growth factor) were increased with higher SPC, while follicle-stimulating and luteinizing hormones decreased. Estrogen receptor α levels were elevated in SPC groups. Vitellogenin gene expression in gonads was highest in Con, while liver expression peaked in LF2. The expression of digestive enzymes, chymotrypsin2, and trypsin2 was highest in LF2, while lipase genes were lower. In summary, up to 50% FM replacement with SPC, with amino acid supplementation, supported growth performance and muscle composition without adverse effects on growth in olive flounder but influenced gonadal development.

The olive flounder, Paralichthys olivaceus, also known as the Korean halibut, is an economically important flatfish in East Asian countries. Here, we provided four fully phased genome assemblies of two different olive flounder individuals using high-fidelity long-read sequencing and their parental short-read sequencing data. We obtained 42–44 Gb of ~15-kb and ~Q30 high-fidelity long reads, and their assembly quality values were ~53. We annotated ~30 K genes, ~170-Mb repetitive sequences, and ~3 M 5-methylcytosine positions for each genome assembly, and established a graph-based draft pan-genome of the olive flounder. We identified 5 M single-nucleotide variants and 100 K structural variants with their genotype information, where ~13% of the variants were possibly fixed in the two Korean individuals. Based on our chromosome-level genome assembly, we also explored chromosome evolution in the Pleuronectiformes family, as reported earlier. Our high-quality genomic resources will contribute to future genomic selection for accelerating the breeding process of the olive flounder.

This study identified the effects of substituting fishmeal (FM) with soy protein concentrate (SPC) supplemented with lysine and methionine in the olive flounder (Paralichthys olivaceus) diet on the expression of genes related to growth, stress, immunity, and digestion. Three experimental diets were prepared; the control diet (Con) contained 60% FM, and the experimental diets contained 25% (SPC25) and 50% (SPC50) FM replaced by SPC. After the 140-day feeding period, weight gain, specific growth rate, feed availability, biological indices, and chemical composition of the muscle were not significantly affected by the dietary treatments. The gene expression levels of growth-related genes (IGF, GFB-3), immune-related genes (IL-8 and caspase), and stress-related genes (SOD, GPX, PRX, TRX) were higher in Con fish than in those fed the SPC25 and SPC50 diets. Chymo-TRY2, TRY2, and TRY3 in the stomach of fish fed the SPC25 diet were higher than fish fed the Con or SPC50 diets. TRY2 and lipase of fish fed the SPC25 diet were higher than those of fish fed the other diets but TRY3 was not significantly affected by the treatments in the intestine. In conclusion, substituting 25% FM with SPC was the most effective diet for the expression of growth, immune, stress, and digestive enzyme genes.

This study identified the effects of substituting fishmeal (FM) with soy protein concentrate (SPC) supplemented with lysine and methionine in the olive flounder (Paralichthys olivaceus) diet on the expression of genes related to growth, stress, immunity, and digestion. Three experimental diets were prepared; the control diet (Con) contained 60% FM, and 25% (SPC25) and 50% (SPC50) FM were replaced by SPC. After the 140-day feeding period, weight gain, specific growth rate, feed availability, biological indices and chemical composition of the muscle were not significantly affected by the dietary treatments. The gene expression levels of growth-related genes (IGF, GFB-3), immune-related genes (IL-8 and caspase), stress-related genes (SOD, GPX, PRX, TRX) were higher in Con fish than in those fed the SPC25 and SPC50 diets. Chymo-TRY2, TRY2 and TRY3 in the stomach of fish fed the SPC25 diet were higher than fish fed the Con or SPC50 diets. TRY2 and lipase of fish fed the SPC25 diet were higher than those of fish fed the other diets but TRY3 was not significantly affected by the treatments in the intestine. In conclusion, substituting 25% FM with SPC was the most effective for the expression of growth, immune, stress, and digestive enzyme genes.

Polymeric immunoglobulin receptor (pIgR) mediates the transfer of polymeric immunoglobulin to protect organisms and is one of the most important mucosal effectors. In this study, the developmental stage- and tissue-specific expression of pIgR were observed before virus inoculation in olive flounder. pIgR was gradually expressed until the formation of immune tissue, exhibiting high expression in the late juvenile period; thereafter, pIgR expression gradually decreased and exhibited high expression in the spleen and skin. Moreover, pIgR expression after viral hemorrhagic septicemia virus infection was high in the kidney and spleen tissues at high density and low at low density. The results of this study can provide a basis for future studies on breeding density, virus expression, and immune system studies in fish.

Ubiquitin-40S ribosomal protein S27a (RPS27A), ubiquitin-like protein Fubi, and ribosomal protein (S30FAU) are ubiquitin-related proteins that are involved in the regulation of immune-related functions such as cell cycle, protein expression, and apoptosis. This study aimed to confirm the molecular characteristics, gene expression analysis, and antibacterial activity of RPS27A and S30FAU identified from the starry flounder (15 starry flounders of 128.7 ± 18.2 g). An expression analysis using a normal fish showed that RPS27A was highly expressed in the head kidney, heart, and stomach. In contrast, S30FAU exhibited high expression in the stomach, heart, and head kidney. Upon simulating an artificial pathogen infection, RPS27A was highly expressed in the heart at 1 h and 3 days post-viral hemorrhagic septicemia (VHSV) infection, and had a high expression in the kidney, liver, and heart at 7 days post-Streptococcus parauberis (S. parauberis) infection. S30FAU was highly expressed in the spleen and gills at 1 day and 12 h post-VHSV infection, respectively, and exhibited a high expression in the kidney at 7 days post-S. parauberis infection. In an MIC analysis, RPS27A and S30FAU showed antimicrobial activity against all bacteria used in this study. In the biofilm assay, S30FAU was removed from S. parauberis in a concentration-dependent manner, and the cytotoxicity test showed no hemolytic activity in both RPS27A and S30FAU. Therefore, RPS27A and S30FAU of the starry flounder were confirmed to possess antimicrobial peptide abilities without limitations of cytotoxicity. This study provides valuable information on the antibacterial ability and molecular biology of the ubiquitin family isolated from the starry flounder.