Complete Genome Sequence of Aeromonas salmonicida subsp. masoucida Strain BR19001YR, Isolated from Diseased Korean Rockfish (Sebastes schlegelii).
ABSTRACT: We report the complete genome sequence of the virulent Aeromonas salmonicida subsp. masoucida strain BR19001YR, isolated from diseased black rockfish (Sebastes schlegelii). Sequencing of the circular chromosome and three plasmids using the PacBio and Illumina platforms yielded 4,982,192 bp with a 58.24% G+C content.
Project description:The recent miniaturization of acoustic tracking devices has allowed fishery managers and scientists to collect spatial and temporal data for sustainable fishery management. The spatial and temporal dimensions of fish behavior (movement and/or vertical migrations) are particularly relevant for rockfishes (Sebastes spp.) because most rockfish species are long-lived and have high site fidelity, increasing their vulnerability to overexploitation. In this study, we describe the short-term (with a tracking period of up to 46 d) spatial behavior, as determined by acoustic tracking, of the black rockfish Sebastes schlegelii, a species subject to overexploitation in the Yellow Sea of China. The average residence index (the ratio of detected days to the total period from release to the last detection) in the study area was 0.92 ± 0.13, and most of the tagged fish were detected by only one region of the acoustic receiver array, suggesting relatively high site fidelity to the study area. Acoustic tracking also suggested that this species is more frequently detected during the day than at night in our study area. However, the diel detection periodicity (24 h) was only evident for certain periods of the tracking time, as revealed by a continuous wavelet transform. The habitat selection index of tagged S. schlegelii suggested that S. schlegelii preferred natural reefs, mixed sand/artificial reef bottoms and mixed bottoms of boulder, cobble, gravel and artificial reefs. The preference of this species for the artificial reefs that were recently deployed in the study area suggests that artificial seascapes may be effective management tools to attract individuals. The vertical movement of tagged S. schlegelii was mostly characterized by bottom dwelling behavior, and there was high individual variability in the vertical migration pattern. Our results have important implications for S. schlegelii catchability, the implementation of marine protected areas, and the identification of key species habitats, and our study provides novel information for future studies on the sustainability of this important marine resource in eastern China.
Project description:Here we report Illumina-based whole genome sequencing of three rockfish species of Sebastes in northwest Pacific. The whole genomic DNA was used to prepare 350-bp pair-end libraries and the high-throughput sequencing yielded 128.5, 137.5, and 124.8 million mapped reads corresponding to 38.54, 41.26, and 37.43?Gb sequence data for S. schlegelii, S. koreanus, and S. nudus, respectively. The k-mer analyses revealed genome sizes were 846.4, 832.5, and 813.1?Mb and the sequencing coverages were 45×, 49×, and 46× for three rockfish, respectively. Comparative genomic analyses identified 46,624 genome-wide single nucleotide polymorphisms (SNPs). Phylogenetic analysis revealed closer relationships of the three species, compared to other six rockfish species. Demographic analysis identified contrasting changes between S. schlegelii and other two species, suggesting drastically different response to climate changes. The reported genome data in this study are valuable for further studies on comparative genomics and evolutionary biology of rockfish species.
Project description:Acute change in water temperature causes heavy economic losses in the aquaculture industry. The present study investigated the metabolic and molecular effects of acute thermal stress on black rockfish (Sebastes schlegelii). Gas chromatography time-of-flight mass spectrometry (GC-TOF-MS)-based metabolomics was used to investigate the global metabolic response of black rockfish at a high water temperature (27°C), low water temperature (5°C) and normal water temperature (16°C). Metabolites involved in energy metabolism and basic amino acids were significantly increased upon acute exposure to 27°C (P < 0.05), and no change in metabolite levels occurred in the low water temperature group. However, certain fatty acid levels were elevated after cold stress (P < 0.05), and this effect was not observed in the 27°C group, suggesting that acute high and low temperature exposures caused different physiological responses. Using quantitative real-time PCR, we analyzed the expression of ubiquitin (ub), hypoxia-inducible factor (hif), lactate dehydrogenase (ldh), and acetyl-CoA carboxylase (acac). Higher expression levels of ub, hif, and ldh (P < 0.05) were observed in the high water temperature group, but no changes in these expression levels occurred in the low water temperature group. Our findings provide a potential metabolic profile for black rockfish when exposed to acute temperature stress and provide some insights into host metabolic and molecular responses to thermal stress.
Project description:<h4>Background</h4>The black rockfish (Sebastes schlegelii) has an ovoviviparous reproductive pattern and long-term sperm storage, resulting in asynchronous gonadal development between the sexes. However, the comprehensive understanding of gonadal development in black rockfish has not yet been achieved. Here, we studied gonadal development and germ cell renewal using histology and RNA-seq.<h4>Results</h4>In this study, RNA-seq was performed on testes and ovaries to characterize key pathways and genes that are active during development and gamete maturation in black rockfish. Differentially expressed genes (DEGs) were identified and annotated in 4 comparisons (F_III vs. F_IV, F_IV vs. F_V, M_III vs. M_IV and M_IV vs. M_V). Based on analysis of DEGs enriched in the testis, 11 and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were mapped to the M_III vs. M_IV group and the M_IV vs. M_V group, respectively. DEGs in ovarian development were also classified into 10 groups according to their biological functions. The expression patterns of the selected genes determined by qPCR were significantly correlated with the RNA-Seq results, supporting the reliability and accuracy of the RNA-Seq analysis. E<sub>2</sub> levels showed down regulation from previtellogenesis to mature stage in female and T level showed down regulation from spermatogenesis to regressed stage in the male.<h4>Conclusions</h4>The categories "intercellular interaction and cytoskeleton", "molecule amplification" and "repair in the cell cycle" were revealed to be crucial in testis development and spermatogenesis, as was the biosynthesis of a series of metabolites. Our results provide comprehensive insight into black rockfish gonadal development and provide a basis for further study of reproductive physiology and molecular biology in ovoviviparity teleosts.
Project description:Microcotyle sebastis is a gill monogenean ectoparasite that causes serious problems in the mariculture of the Korean rockfish, Sebastes schlegelii. In this study, we isolated the parasite from fish farms along the coasts of Tongyeong, South Korea in 2016, and characterized its infection, morphology and molecular phylogeny. The prevalence of M. sebastis infection during the study period ranged from 46.7% to 96.7%, and the mean intensity was 2.3 to 31.4 ind./fish, indicating that the fish was constantly exposed to parasitic infections throughout the year. Morphological observations under light and scanning electron microscopes of the M. sebastis isolates in this study showed the typical characteristics of the anterior prohaptor and posterior opisthaptor of monogenean parasites. In phylogenetic trees reconstructed using the nuclear 28S ribosomal RNA gene and the mitochondrial cytochrome c oxidase I gene (cox1), they consistently clustered together with their congeneric species, and showed the closest phylogenetic relationships to M. caudata and M. kasago in the cox1 tree.
Project description:Germ cells play a key role in gonad development. As precursors, primordial germ cells (PGCs) are particularly important for germline formation. However, the origination and migration patterns of PGCs are poorly studied in marine fish, especially for viviparous economic species. The <i>vasa</i> gene has been widely used as a germ cell marker to identify a germline because <i>vasa</i> RNA is a component of germ plasm. In this study, we described the expression pattern of black rockfish (<i>Sebastes schlegelii</i>) <i>vasa</i> (<i>Ssvas</i>) in gonadal formation and development by <i>in situ</i> hybridization. The results showed that <i>Ssvas</i> failed in localization at the cleavage furrows until the late gastrula stage, when PGCs appeared and migrated to the genital ridge and formed elongated gonadal primordia at 10 days after birth. This study firstly revealed the PGCs origination and migration characteristics in viviparous marine fish. Furthermore, we microinjected chimeric mRNA containing EGFP and the 3'untranslated region (3'UTR) of <i>Ssvas</i> into zebrafish (<i>Danio rerio</i>) and marine medaka (<i>Oryzias melastigma</i>) fertilized eggs for tracing PGCs. We found that, although <i>Sebastes schlegelii</i> lacked early localization, similar to red seabream (<i>Pagrus major</i>) and marine medaka, only the 3'UTR of <i>Ssvas vasa</i> 3'UTR of black rockfish was able to label both zebrafish and marine medaka PGCs. In comparison with other three Euteleostei species, besides some basal motifs, black rockfish had three specific motifs of M10, M12, and M19 just presented in zebrafish, which might play an important role in labeling zebrafish PGCs. These results will promote germ cell manipulation technology development and facilitate artificial reproduction regulation in aquaculture.
Project description:Myosins are important eukaryotic motor proteins that bind actin and utilize the energy of ATP hydrolysis to perform a broad range of functions such as muscle contraction, cell migration, cytokinesis, and intracellular trafficking. However, the characterization and function of <i>myosin</i> is poorly studied in teleost fish. In this study, we identified 60 <i>myosin</i> family genes in a marine teleost, black rockfish (<i>Sebastes schlegelii</i>), and further characterized their expression patterns. <i>myosin</i> showed divergent expression patterns in adult tissues, indicating they are involved in different types and compositions of muscle fibers. Among 12 subfamilies, <i>S. schlegelii myo2</i> subfamily was significantly expanded, which was driven by tandem duplication events. The up-regulation of five representative genes of <i>myo2</i> in the skeletal muscle during fast-growth stages of juvenile and adult <i>S. schlegelii</i> revealed their active role in skeletal muscle fiber synthesis. Moreover, the expression regulation of <i>myosin</i> during the process of myoblast differentiation <i>in vitro</i> suggested that they contribute to skeletal muscle growth by involvement of both myoblast proliferation and differentiation. Taken together, our work characterized <i>myosin</i> genes systemically and demonstrated their diverse functions in a marine teleost species. This lays foundation for the further studies of muscle growth regulation and molecular mechanisms of indeterminate skeletal muscle growth of large teleost fishes.
Project description:Here, we report the complete genome sequence of the pathogenic Aeromonas salmonicida subsp. masoucida strain RFAS1, isolated from black rockfish and showing signs of furunculosis. Sequencing with the PacBio platform yielded a circular chromosome of 4,783,004?bp and two plasmids (70,968?bp and 63,563?bp) harboring 4,411, 67, and 71 protein-coding genes, respectively.
Project description:The mammalian target of rapamycin (mTOR) is an evolutionarily highly conserved atypical serine/threonine protein kinase, which regulates cell growth, proliferation, apoptosis, autophagy, and metabolism. As a regulatory protein, Raptor is awfully important for the stability and function of mTOR complex 1 (mTORC1). However, the studies about how Raptor/mTORC1 participates in and regulates immune response in lower vertebrates are still limited. In this study, we investigated the regulation of immune response by the Raptor/mTORC1 signaling pathway in rockfish Sebastes schlegelii. Sebastes schlegelii Raptor (Ss-Raptor) is a highly conserved protein during the evolution, in both primary and tertiary structure. Ss-Raptor mRNA was widely distributed in various tissues of rockfish and has a relative higher expression in spleen and blood. After infected by Micrococcus luteus or Listonella anguillarum, mRNA expression of Ss-Raptor rapidly increased within 48 h. Once Raptor/mTORC1 signaling was blocked by rapamycin, expression of the pro-inflammatory cytokines IL-1? and IL-8 was severely impaired, suggesting potential regulatory role of Raptor/mTORC1 signaling in the innate immune response of rockfish. In addition, Raptor/mTORC1 pathway participated in lymphocyte activation of rockfish through promoting 4EBP1 and S6 phosphorylation. Inhibition of Raptor/mTORC1 signaling crippled the lymphocyte expansion during primary adaptive immune response, manifesting by the decrease of lymphoid organ weight and lymphocyte numbers. More importantly, inhibition of Raptor/mTORC1 signaling impaired the lymphocyte mediated cytotoxic response, and made the fish more vulnerable to the bacterial infection. Together, our results suggested that Raptor and its tightly regulated mTORC1 signaling acts as modulatory center to regulate both innate and lymphocyte-mediated adaptive immune response during bacterial infection. This research has shed new light on regulatory mechanism of teleost immune response, and provide helpful evidences to understand the evolution of immune system.
Project description:Marine reserves networks are implemented as a way to mitigate the impact of fishing on marine ecosystems. Theory suggests that a reserve network will function synergistically when connected by dispersal, but the scale of dispersal is often unknown. On the Pacific coast of the United States and Canada, both countries have recently implemented a number of rockfish conservation areas (RCAs) to protect exploited rockfish species, but no study has evaluated the connectivity within networks in each country or between the two countries. We used isolation-by-distance theory to estimate the scale of dispersal from microsatellite data in the black rockfish, Sebastes melanops, and compared this estimate with the distance between RCAs that would protect this species. Within each country, we found that the distance between RCAs was generally within the confidence intervals of mean dispersal per generation. The distance between these two RCA networks, however, was greater than the average dispersal per generation. The data were also consistent with a genetic break between southern Oregon and central Oregon. We discuss whether additional nearshore RCAs in southern Oregon and Washington would help promote connectivity between RCA's for shallow-water rockfishes.