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Veneroida is the largest order of bivalves, and these clams are commercially important in Asian countries. Although numerous studies have focused on the genomic characters of individual species or genera in Veneroida, superfamily-specific genomic characters have not been determined. In this study, we performed a comparative genomic analysis of 12 mitochondrial protein coding genes (PCGs) from 25 clams in six Veneroida superfamilies to determine genomic and evolutionary features of each superfamily. Length and distribution of nucleotides encoding the PCGs were too variable to define superfamily-specific genomic characters. Phylogenetic analysis revealed that PCGs are suitable for classification of species in three superfamilies: Cardioidea, Mactroidea, and Veneroidea. However, one species classified in Tellinoidea, Sinonovacula constricta , was evolutionarily closer to Solenoidea clams than Tellinoidea clams. dN/dS analysis showed that positively selected sites in NADH dehydrogenase subunit, nd4 and subunit of ATP synthase, atp6 were present in Mactroidea. Differences in selected sites in the nd4 and atp6 could be caused by superfamily-level differences in sodium transport or ATP synthesis functions, respectively. These differences in selected sites in NADH may have conferred these animals, which have low motility and do not generally move, with increased flexibility to maintain homeostasis in the face of osmotic pressure. Our study provides insight into evolutionary traits as well as facilitates identification of veneroids. [ABSTRACT FROM AUTHOR]

The potential impact of natural and synthetic estrogens on aquatic ecosystems has become a subject of great interest in recent years. One synthetic estrogen, 17-alpha-ethinylestradiol (EE2), is present in municipal sewage discharges and causes gonad alterations in various fish species. To understand the possible damage caused by EE2, male Rhodeus uyekii were exposed to 100 ng/L EE2 for 7 days. RNA-Seq was performed to assess the effects of EE2 on gene expression in hepatic and skin tissues. The analysis revealed that EE2 induced the expression of various genes, including sex hormone genes, anti-Mullerian hormone, vitellogenin, and estrogen receptor alpha; cancer genes, breast cancer anti-estrogen resistance protein 3, caveolin 2, and Smad2; and apoptotic genes, p53, Bcl-2, TNF-α, and WDR36. These results suggest that the synthetic estrogen EE2 disturbs the endocrine system and regulates both carcinogenic and apoptotic gene expressions in R. uyekii . [ABSTRACT FROM AUTHOR]

Abstract: This is the first study to report the concentrations and accumulation profiles of PFCs in marine mammals from Korea. The concentrations and profiles of 10 PFCs in the liver of minke whales and common dolphins from Korean coastal waters were recorded in this study. The mean concentrations of PFOS and PFUnDA were 3–20 times higher than that found for other PFCs analyzed. The concentrations of PFOS in cetaceans from Korea were relatively lower than those reported in other countries. Inter-species differences in the concentrations of PFOS, PFOSA and PFNA were found between two cetacean species, while no difference was observed in the concentrations of PFDA, PFUnDA and PFDoDA between the species. The dominant PFC compounds found in cetaceans were PFUnDA and PFOS, accounting for 70–80% of the PFCs. The accumulation profiles and correlation analysis indicated that two cetacean species have different exposure routes and metabolic capacity for PFCs. [Copyright &y& Elsevier]

Among the 14 species in the Acetes genus, Acetes japonicus and Acetes chinensis , are the only and also abundant two species around the Korean Peninsula, and are used in traditional recipes. These species are of great economic importance, but little is known about their population genetics, despite the fact that information of this kind is important for stock assessment, fisheries management and identification of origin. A total of 9 microsatellite (MS) markers for A. chinensis were developed using pyrosequencing techniques. Polymorphisms of these markers were evaluated in 96 wild individuals collected from the Yellow Sea off the coast of Korea. A total of 133 alleles were detected at nine loci, with a cross-species transferability of 56% with A. japonicus . These markers will facilitate assessment of population genetic diversity in the genus Acetes . [ABSTRACT FROM AUTHOR]

The increased international trade and worldwide consumption of seafood has increased the possibility of economic fraud. Particularly, the increased development of processed seafood has restricted the application of classical identification methods. DNA matabarcoding is a rapid method for identification of multiple species from an environmental sample. In this study, two universal markers were designed in the mitochondrial cytochrome oxidase subunit I region, and the metabarcoding analysis of processed seafood products was done using these markers. A total of 11 seafood products were analyzed, and 56 and 32 species within 36 families between them were identified by each primer set, respectively. Comparing the identified species with each primer set, only 12.8% of the species were identified by both primer sets. In addition, the species on the label when identified were not observed in some products. Although the analysis was done on the same gene region, different results can be obtained according to the primer set. Based on these results, it is advantageous to use more than one primer set to identify various species from seafood products using DNA metabarcoding analysis. • High throughput metabarcoding was the most promising method for species identification in processed seafood. • DNA metabarcoding can allow the identification of various raw materials in mixed products. • Eleven seafood products were tested using the metabarcoding method with two universal primer sets. • The results indicated the presence of incorrectly labeled processed seafood products. [ABSTRACT FROM AUTHOR]

Highlights • A method was established for the quantitative analysis of Alaska pollock from processed seafoods. • 16S rRNA region was used as a DNA marker for quantitative analysis. • A formula was devised to determine the weight of Alaska pollock based on the DNA copy number. • The method was applied successfully to the analysis of 15 processed seafoods. Abstract A highly accurate quantitative method, based on the new technique, droplet digital PCR (ddPCR), was applied to determine the content of Alaska pollock (Gadus chalcogrammus) in seafood products. Using this method, we found a linear relationship among raw sample weight, DNA concentration and DNA copy number. We also established a formula to calculate the raw sample weight, based on the number of DNA copies. To confirm the accuracy and applicability of this method, mixed samples of known composition were analyzed. Results from this study indicated that the ddPCR method described is suitable for quantifying Alaska pollock in seafood products and has the potential applied to a variety of tasks in food quality certification. [ABSTRACT FROM AUTHOR]

We isolated and characterised a cDNA encoding the lysosomal protective protein (serine protease) cathepsin A (CTSA) from rock bream ( Oplegnathus fasciatus ). The full-length rock bream CTSA (RbCTSA) cDNA (1814 bp) contains an open reading frame of 1419 bp that encodes 472 amino acids. Alignment of multiple CTSA protein sequences revealed that the active site serine and histidine residues were well-conserved among the other CTSA sequences. RbCTSA is highly expressed in the peripheral blood leukocytes, kidney, spleen, liver, intestine, gill, heart, brain, stomach, and eye. RbCTSA expression was also examined in several tissues, including whole kidneys and spleens, under bacterial and viral challenge. In general, all of the examined tissues that were infected with Edwardsiella tarda , Streptococcus iniae , or red sea bream iridovirus (RSIV) exhibited significant upregulation of RbCTSA expression compared to the controls. Our results reveal that RbCTSA may be involved in the immune responses of rock bream. [ABSTRACT FROM AUTHOR]

The purpose of this study was to develop a DNA marker for the identification of fish species in processed surimi products. A DNA marker was designed based on the mitochondrial cytochrome c oxidase subunit I gene, and fish species in surimi products were identified using a molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE); the results were subjected to sequence-based analysis. The DGGE profiles indicated the presence in surimi products of a greater diversity of fish species than reported previously: 20 species belonging to 16 genera were identified. Therefore, our method facilitates the simple and rapid detection and identification of fish species in seafood products produced from minced fish. [ABSTRACT FROM AUTHOR]

Abstract: Large amounts of the manila clam, Ruditapes philippinarum, have been imported from Dalian (China) recently to meet the increasing demand in Korea. To ensure the quality and safety of the domestic marine product, it is necessary to be able to distinguish between domestic manila clams and clams that are imported from Dalian, China. We developed expressed sequence tags (ESTs)-derived single nucleotide polymorphism markers using 454 pyrosequencing. A total of 780,000 ESTs were assembled, and 49,540 putative SNPs were identified from 46,405 contigs. Twenty-one polymorphic SNPs from 11 primers were finally selected as diagnostic markers. Genotype analysis showed that 21 SNP markers had the opposite alleles (transitions or transversions) between domestic and imported samples, which were useful for distinguishing clam origins. The GENECLASS 2.0 program was used to estimate the ability of the markers in the discrimination between domestic and imported populations. The 21 SNP markers had 98.96% ability to discriminate domestic manila clams and 100% ability to identify those imported. These markers could be useful for discriminating between domestic and imported manila clams and can contribute to the prevention of falsified labeling of this species. [Copyright &y& Elsevier]

Abstract: Two species of mitten crab, Eriocheir sinensis and Eriocheir japonica, are commercially valuable in Korea. Millions of their juveniles have been released in attempts to restore ecological habitat and enhance fishery resources. Due to their habitat's singularity, exact species identification should be conducted before juveniles are released. In this study, we used a highly conserved region of the mitochondrial cytochrome b (cyt b) gene to distinguish E. sinensis from E. japonica. We designed a primer set to amplify part of the mitochondrial cyt b gene of both species and obtained 1024 base pairs (bp) of polymerase chain reaction (PCR) product. These PCR products were digested with the restriction enzyme MboII and the species-specific restriction fragment length polymorphism (RFLP) patterns were analyzed. Also, we designed primers for the rapid identification of cyt b gene (498 bp) to distinguish E. sinensis. PCR-RFLP and PCR using new primers are a fast and inexpensive method to access species identification. This simple and rapid method can provide useful information for E. sinensis and E. japonica species identification. [Copyright &y& Elsevier]

Abstract: Despite several studies that report accumulation of polychlorinated biphenyls (PCBs) and DDT in marine mammals worldwide, very few have examined polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and dioxin-like PCBs. In particular, no earlier studies have reported concentrations and accumulation profiles of persistent organic pollutants (POPs) in marine mammals from Korea. In this study, concentrations and accumulation features of PCDD/Fs and dioxin-like PCBs were measured in liver and blubber of minke whales and long-beaked common dolphins collected from Korean coastal waters. The concentrations of PCDFs and dioxin-like PCBs in blubber were 3–10 times higher than the concentrations measured in liver, but PCDDs were higher in liver than blubber. Total toxic equivalent (TEQ) concentrations in blubber of minke whales and common dolphins from Korean coastal waters were similar to, or higher than those reported for cetaceans and seals from other countries. Homologue and congener profiles of PCDD/Fs were different between livers and blubbers, while the profiles of dioxin-like PCBs were similar between the tissues. Concentrations of PCDD/Fs and dioxin-like PCBs in liver and blubber of dolphins were significantly higher than those measured in whales, due to differences in habitat and diet. The relative contribution of individual chemical groups to total TEQs was different between the two cetacean species, suggesting different exposures and metabolic activity. The TEQ levels in minke whales did not exceed the threshold level suggested for immunomodulation, while TEQs in all dolphin samples exceeded the suggested threshold level, implying potential adverse health effects from exposure to PCDD/Fs and PCBs. [Copyright &y& Elsevier]

We isolated and characterised a cDNA encoding the aspartic protease cathepsin E (CTSE) in Korean rose bitterling, Rhodeus uyekii. The full-length Rhodeus uyekii CTSE (RuCTSE) cDNA (1396 bp) contains an open reading frame of 1218 bp, encoding 405 amino acids. Alignment of multiple CTSE protein sequences revealed that two of the aspartyl protease active site residues and a disulphide bond were well-conserved among the other CTSE sequences. Phylogenetic analysis revealed that RuCTSE is most closely related to freshwater fish cathepsin E. RuCTSE is widely expressed in the liver, spleen, ovary, testis, brain, eye, intestine, muscle, fin, stomach, and kidney. This first report of teleost CTSE will provide important information related to the identification of other cathepsin E genes in various fish species and will serve as a useful molecular tool to help clarify biological activities in other teleosts. • The cathepsin E (CTSE) cDNA was identified from a Korean rose bitterling. • Two aspartyl protease active sites and disulphide bond were well-conserved within the aligned sequence. • The newly identified RuCTSE is a member of the aspartic protease superfamily through phylogenetic analysis. • RuCTSE gene was highly expressed in the liver, spleen, and ovary. [ABSTRACT FROM AUTHOR]