Korean Ocean Research and Development Institute

About: Korean Ocean Research and Development Institute is a facility organization based out in Busan, South Korea. It is known for research contribution in the topics: Sea surface temperature & Gene. The organization has 1770 authors who have published 3032 publications receiving 50142 citations.

Chromosomal-level assembly of Takifugu obscurus (Abe, 1949) genome using third-generation DNA sequencing and Hi-C analysis.

Abstract: The Tetraodontidae family are known to have relatively small and compact genomes compared to other vertebrates. The obscure puffer fish Takifugu obscurus is an anadromous species that migrates to freshwater from the sea for spawning. Thus the euryhaline characteristics of T. obscurus have been investigated to gain understanding of their survival ability, osmoregulation, and other homeostatic mechanisms in both freshwater and seawater. In this study, a high quality chromosome-level reference genome for T. obscurus was constructed using long-read Pacific Biosciences (PacBio) Sequel sequencing and a Hi-C-based chromatin contact map platform. The final genome assembly of T. obscurus is 381 Mb, with a contig N50 length of 3,296 kb and longest length of 10.7 Mb, from a total of 62 Gb of raw reads generated using single-molecule real-time sequencing technology from a PacBio Sequel platform. The PacBio data were further clustered into chromosome-scale scaffolds using a Hi-C approach, resulting in a 373 Mb genome assembly with a contig N50 length of 15.2 Mb and and longest length of 28 Mb. When we directly compared the 22 longest scaffolds of T. obscurus to the 22 chromosomes of the tiger puffer Takifugu rubripes, a clear one-to-one orthologous relationship was observed between the two species, supporting the chromosome-level assembly of T. obscurus. This genome assembly can serve as a valuable genetic resource for exploring fugu-specific compact genome characteristics, and will provide essential genomic information for understanding molecular adaptations to salinity fluctuations and the evolution of osmoregulatory mechanisms.

Enhanced Hydrogen-Storage Capacity and Structural Stability of an Organic Clathrate Structure with Fullerene (C60) Guests and Lithium Doping

Abstract: An effective combination of host and guest molecules in a framework type of architecture can enhance the structural stability and physical properties of clathrate compounds. We report here that an organic clathrate compound consisting of a fullerene (C60) guest and a hydroquinone (HQ) host framework shows enhanced hydrogen-storage capacity and good structural stability under pressures and temperatures up to 10 GPa and 438 K, respectively. This combined structure is formed in the extended β-type HQ clathrate and admits 16 hydrogen molecules per cage, leading to a volumetric hydrogen uptake of 49.5 g L–1 at 77 K and 8 MPa, a value enhanced by 130% compared to that associated with the β-type HQ clathrate. A close examination according to density functional theory calculations and grand canonical Monte Carlo simulations confirms the synergistic combination effect of the guest–host molecules tailored for enhanced hydrogen storage. Moreover, the model simulations demonstrate that the lithium-doped HQ clathrates...

DNA-barcoding of perch-like fishes (Actinopterygii: Perciformes) from far-eastern seas of Russia with taxonomic remarks for some groups

Abstract: The analysis of variation among 203 nucleotide sequences of Co-1 gene (DNA-barcode) for 45 species, 31 genera and 7 families of the order Perciformes from the Far Eastern seas of Russia has been performed. As a result, 42 species (93.3%) can be unambiguously identified using molecular DNA-barcode at Co-1, whereas more variable markers are required for other species (6.7%): Stichaeus grigorjewi, S. nozawae, and Lumpenus sagitta. The latter includes as well 2 morphologically distinct (by number of vertebrae) but genetically unresolved species, L. sagitta (Sea of Okhotsk) and L. fabricii (Bering Sea). In addition, within this genus morphologically poorly characterized but genetically well-distinguished cryptic species has been detected. Amphi-Pacific distribution is in question relative to L. sagitta. Cryptic diversity was observed in the genus Ammodytes.

De novo transcriptome assembly of brackish water flea Diaphanosoma celebensis based on short-term cadmium and benzo[a]pyrene exposure experiments.

Abstract: To develop a brackish water flea as a promising model for marine monitoring, Diaphanosoma celebensis were exposed to two pollutants, cadmium (Cd) and benzo[a]pyrene (BaP), which have different chemical characteristics and distinct modes of metabolic action on aquatic animals. Twenty-four hours after exposure to Cd (2 mg/L) or BaP (25 μg/L), whole body transcriptomes were analyzed. In total, 99.6 Mbp were assembled from nine libraries, resulting in 98,458 transcripts with an N50 of 1883 bp and an average contig length of 968 bp. Functional gene annotations were performed using Gene Ontology, Eukaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes pathway analyses. Cd significantly modulated endocrine and digestive enzyme system. Following BaP treatment, DNA repair and circadian rhythm related metabolisms were significantly modulated. Both the chemicals induced stress response and detoxification metabolism. This brackish water flea genomic information will be useful to monitor estuaries and coastal regions, as water fleas have been confirmed as promising sentinel models in freshwater ecosystems.

The influence of coastal waters on distributions of heterotrophic protists in the northern East China Sea, and the impact of protist grazing on phytoplankton

Abstract: Spatial and temporal variations in the abundance and biomass of heterotrophic protists and of their grazing impact were investigated during five cruises between July 2006 and February 2009 in the continental shelf waters of the northern East China Sea (ECS). Strongly patchy distributions were observed on all cruises, generally with a higher biomass in the western areas affected by the Changjiang River discharge. An opposite pattern was observed in February when the Kuroshio onshore transport is greatest, with a greater biomass in the eastern area. Small heterotrophic dinoflagellates (,20 mm) were most abundant numerically, whereas ciliates contributed the most to the biomass, accounting for 28–58% of the total heterotrophic protist biomass. Small heterotrophic dinoflagellates were more strongly correlated with phytoplankton biomass than were other types of protists. The total protist biomass was often most strongly related to amounts of particulate organic carbon of non-phytoplankton origin, suggesting that their abundance distribution often depended on prey other than phytoplankton, such as heterotrophic bacteria. Heterotrophic protists consumed 30.1–91.5% of Chl a production (mean 68.2%), with grazing rates increasing with the phytoplankton biomass. The results suggest that heterotrophic protists were the major consumers of primary production, and that their grazing is one of the most important losses affecting the phytoplankton biomass in the northern ECS.