Draft Genome Sequence of Vibrio harveyi Strain GAN1807, Isolated from Diseased Greater Amberjack (Seriola dumerili) Farmed in Nomi Bay, Japan, in 2018.
Ontology highlight
ABSTRACT:
SUBMITTER: Kato Y
PROVIDER: S-EPMC6706684 | biostudies-literature | 2019 Aug
REPOSITORIES: biostudies-literature
Publications
Draft Genome Sequence of Vibrio harveyi Strain GAN1807, Isolated from Diseased Greater Amberjack (Seriola dumerili) Farmed in Nomi Bay, Japan, in 2018.
Kato Yusuke Y Wada Takayuki T Yamashita Hazuki H Ikeda Takuji T Nishiyama Kei K Imajoh Masayuki M
Microbiology resource announcements 20190822 34
<i>Vibrio harveyi</i> is a Gram-negative, bioluminescent bacterium within the family <i>Vibrionaceae</i> Here, we report the draft genome sequence of <i>V. harveyi</i> strain GAN1807, which was isolated from a diseased greater amberjack (<i>Seriola dumerili</i>) with symptoms of <i>V. harveyi</i>-associated vibriosis in Nomi Bay in Japan. ...[more]
Similar Datasets
Project description:Here, we report the complete genome sequence of a potentially new serotype, Lactococcus garvieae strain MS210922A, isolated from greater amberjack. It is nonreactive to serotype I or II antisera. The complete genome comprises 2,007,159 bp, including 1,929 coding, 16 rRNA, and 58 tRNA genes, with 38.9% G+C content.
| S-EPMC9753671 | biostudies-literature
Project description:The sex determination systems of fish are highly diverse compared with those of mammals. Thus, performing investigations using nonmodel fish species helps to understand the highly diverse sex determination systems of fish. Because greater amberjack (Seriola dumerili) is one of the most important edible fish globally and knowledge of its sex determination system is economically important in the field of aquaculture, we are interested in the mechanisms of sex determination of Seriola species. In this study, we identified sex-associated SNPs of greater amberjack using SNP information of 10 males and 10 females by an association test. We determined that the sex-associated SNPs were on chromosome 12 and mainly covered with two scaffolds (about 7.1 Mbp). Genotypes of sex-associated SNPs indicated that females are the heterogametic sex (ZZ/ZW). Furthermore, we compared the genomic structure of greater amberjack with those of Japanese amberjack (Seriola quinqueradiata), California yellowtail (Seriola dorsalis), and medaka (Oryzias latipes). Whole-genome alignments and synteny analysis indicated that the sex determination system of greater amberjack is markedly different from that of medaka and implied that the sex determination system is conserved in the Seriola species.
| S-EPMC5970132 | biostudies-literature
Project description:Background:Teleosts of the genus Seriola, commonly known as amberjacks, are of high commercial value in international markets due to their flesh quality and worldwide distribution. The Seriola species of interest to Mediterranean aquaculture is the greater amberjack (Seriola dumerili). This species holds great potential for the aquaculture industry, but in captivity, reproduction has proved to be challenging, and observed growth dysfunction hinders their domestication. Insights into molecular mechanisms may contribute to a better understanding of traits like growth and sex, but investigations to unravel the molecular background of amberjacks have begun only recently. Findings:Illumina HiSeq sequencing generated a high-coverage greater amberjack genome sequence comprising 45 909 scaffolds. Comparative mapping to the Japanese yellowtail (Seriola quinqueriadiata) and to the model species medaka (Oryzias latipes) allowed the generation of in silico groups. Additional gonad transcriptome sequencing identified sex-biased transcripts, including known sex-determining and differentiation genes. Investigation of the muscle transcriptome of slow-growing individuals showed that transcripts involved in oxygen and gas transport were differentially expressed compared with fast/normal-growing individuals. On the other hand, transcripts involved in muscle functions were found to be enriched in fast/normal-growing individuals. Conclusion:The present study provides the first insights into the molecular background of male and female amberjacks and of fast- and slow-growing fish. Therefore, valuable molecular resources have been generated in the form of a first draft genome and a reference transcriptome. Sex-biased genes, which may also have roles in sex determination or differentiation, and genes that may be responsible for slow growth are suggested.
| S-EPMC5751066 | biostudies-literature
Project description:Ambient salinity is one of the crucial abiotic factors that poses substantial impacts on fish growth, development and reproduction. Greater amberjack (Seriola dumerili) is of high economic value because, and its reproduction and survival are sensitive to water salinity. To better understand the molecular adaptive mechanism to salinity fluctuations in greater amberjack, we performed comparative transcriptome analysis for gill and kidney between the optimum salinity (30 ppt, CK) and undesired regimes (10 and 40 ppt). For the gill, the skeletal development was provoked upon either hypo- or hyper-salinity stimuli, and the development of pronephros, as well as vascular endothelial cells and cortisol-mediated mitochondria-rich cell, was activated in response to the salinity alterations in kidney. These enhancements may encourage the maintenance of the gill and kidney structures and alleviate the salinity-induced damage. Ion channels NKCC1 and CFTR and the transporters for ammonium and other substances were highly upregulated in the gills and kidney, respectively, which act important roles in the osmoregulation of greater amberjack. More important, undesirable alterations of ambient salinity were found to pose adverse impacts on the immune function of greater amberjack, which may increase the risk of pathogen infection and reduce the security and yield of aquaculture of greater amberjack. In addition, deviation from the optimum salinity condition may result in undesirable uptake and accumulation of environmental toxins in greater amberjack, which attracts further attention to the food safety. Collectively, these novel findings advance our knowledge on adaptative mechanisms to ambient salinity oscillations in greater amberjack and provide a theoretical guidance for the optimal breeding mode for the aquaculture of greater amberjack.
2023-06-24 | GSE220485 | GEO
Project description:The greater amberjack Seriola dumerili is a large teleost fish with rapid growth and excellent flesh quality, whose domestication represents an ambitious challenge for aquaculture. The occurrence of reproductive dysfunctions in greater amberjack reared in captivity was investigated by comparing reproductive development of wild and captive-reared individuals. Wild and captive-reared breeders were sampled in the Mediterranean Sea during three different phases of the reproductive cycle: early gametogenesis (EARLY, late April-early May), advanced gametogenesis (ADVANCED, late May-early June) and spawning (SPAWNING, late June-July). Fish reproductive state was evaluated using the gonado-somatic index (GSI), histological analysis of the gonads and determination of sex steroid levels in the plasma, and correlated with leptin expression in the liver and gonad biochemical composition. The GSI and sex steroid levels were lower in captive-reared than in wild fish. During the ADVANCED period, when the wild greater amberjack breeders were already in spawning condition, ovaries of captive-reared breeders showed extensive atresia of late vitellogenic oocytes and spermatogenic activity ceased in the testes of half of the examined males. During the SPAWNING period, all captive-reared fish had regressed gonads, while wild breeders still displayed reproductive activity. Liver leptin expression and gonad proximate composition of wild and captive greater amberjack were similar. However, the gonads of captive-reared fish showed different total polar lipid contents, as well as specific lipid classes and fatty acid profiles with respect to wild individuals. This study underlines the need for an improvement in rearing technology for this species, which should include minimum handling during the reproductive season and the formulation of a specific diet to overcome the observed gonadal decrements of phospholipids, DHA (22:6n-3) and ARA (20:4n-6), compared to wild breeders.
| S-EPMC5215828 | biostudies-literature
Project description:A 8-week feeding trial was conducted to determine the effects of dietary supplementation with curcumin on growth, intestinal health, and gills resistance to ammonia stress in juvenile Seriola dumerili. Three isonitrogenous and isolipidic test diets were prepared by supplementing incremental levels of dietary curcumin at 0% (CUR0%, control), 0.01% (CUR0.01%), 0.02% (CUR0.02%), respectively. Fish were fed with experimental diet. Recovery and protection capacity after ammonia challenge assay was adopted to test the effect of curcumin. At the end of the feeding trial, the results showed that dietary supplementation with proper curcumin level had a significant positive effect on fish survival and intestinal histology structure. Meanwhile, dietary supplementation with proper curcumin level can improve intestinal health by increasing immune enzyme activity, up-regulating the expression of anti-inflammatory cytokines, down-regulating the expression of pro-inflammatory cytokines and regulating other immune-related genes. Subsequently, after the ammonia challenge and recovery experiment, the results of antioxidant-related genes and antioxidant enzymes showed that dietary supplementation with proper curcumin level can improve the gill protective and recovery capacity from ammonia stress through increasing antioxidant capacity. These results suggest that dietary supplementation with proper curcumin can promote the growth, intestinal health, gill resistance and recovery to ammonia stress of S. dumerili.
| S-EPMC9712565 | biostudies-literature
Project description:Salinity significantly affects physiological and metabolic activities, breeding, development, survival, and growth of marine fish. The greater amberjack (Seriola dumerili) is a fast-growing species that has immensely contributed to global aquaculture diversification. However, the tolerance, adaptation, and molecular responses of greater amberjack to salinity are unclear. This study reared greater amberjack juveniles under different salinity stresses (40, 30, 20, and 10 ppt) for 30 days to assess their tolerance, adaptation, and molecular responses to salinity. RNA sequencing analysis of gill tissue was used to identify genes and biological processes involved in greater amberjack response to salinity stress at 40, 30, and 20 ppt. Eighteen differentially expressed genes (DEGs) (nine upregulated and nine downregulated) were identified in the 40 vs. 30 ppt group. Moreover, 417 DEGs (205 up-regulated and 212 down-regulated) were identified in the 20 vs. 30 ppt group. qPCR and transcriptomic analysis indicated that salinity stress affected the expression of genes involved in steroid biosynthesis (ebp, sqle, lss, dhcr7, dhcr24, and cyp51a1), lipid metabolism (msmo1, nsdhl, ogdh, and edar), ion transporters (slc25a48, slc37a4, slc44a4, and apq4), and immune response (wnt4 and tlr5). Furthermore, KEGG pathway enrichment analysis showed that the DEGs were enriched in steroid biosynthesis, lipids metabolism, cytokine-cytokine receptor interaction, tryptophan metabolism, and insulin signaling pathway. Therefore, this study provides insights into the molecular mechanisms of marine fish adaptation to salinity.
| S-EPMC8833429 | biostudies-literature
Project description:The greater amberjack (Seriola dumerili) is a gonochoristic fish with no sexual dimorphism in appearance, making sex identification difficult. Piwi-interacting RNAs (piRNAs) function in transposon silencing and gametogenesis and are involved in various physiological processes, including sex development and differentiation. Exosomal piRNAs can be indicators for the determination of sex and physiological status. In this study, four piRNAs were differentially expressed in both serum exosomes and gonads between male and female greater amberjack. Three piRNAs (piR-dre-32793, piR-dre-5797, and piR-dre-73318) were significantly up-regulated and piR-dre-332 was significantly down-regulated in serum exosomes and gonads of male fish, compared to female fish, consistent with the serum exosomal results. According to the relative expression of four marker piRNAs derived from the serum exosomes of greater amberjack, the highest relative expression of piR-dre-32793, piR-dre-5797, and piR-dre-73318 in seven female fish and that of piR-dre-332 in seven male fish can be used as the standard for sex determination. The method of sex identification can ascertain the sex of greater amberjack by blood collection from the living body, without sacrificing fish. The four piRNAs did not show sex-inclined expression in the hypothalamus, pituitary, heart, liver, intestine, and muscle tissue. A piRNA-target interaction network involving 32 piRNA-mRNA pairs was generated. Sex-related target genes were enriched in sex-related pathways, including oocyte meiosis, transforming growth factor-beta signaling pathway, progesterone-mediated oocyte maturation, and gonadotropin releasing hormone signaling pathway. These results provide a basis for sex determination in greater amberjack and improve our understanding of the mechanisms underlying sex development and differentiation in the species.
| S-EPMC9962539 | biostudies-literature
Project description:The greater amberjack (Seriola dumerili), a pelagic marine species with a global distribution, has considerable worldwide potential as an aquaculture species. However, difficulties have been encountered in inducing spontaneous spawning in cultured fish stocks. In this study, we analysed the key regulatory factors, secretoneurin (SN) and gonadotropin-releasing hormone (GnRH), in greater amberjack. Active peptides of SN and GnRH, SdSNa, and SdGnRH, respectively, were obtained by comparative analysis of homologous proteins from different species. Amino acid substitutions of the SdGnRH decapeptide at position 6 with a dextrorotatory (D) amino acid and at position 10 with an ethylamide group yielded a super-active agonist (SdGnRHa). The injection of SdSNa and SdGnRHa elevated luteinizing hormone, thyroid-stimulating hormone, and oxytocin levels in the sera of sexually mature fish, whereas it reduced the level of follicle-stimulating hormone. Furthermore, in response to the SdSNa and SdGnRHa injections, we detected an increase in the expression of genes associated with oocyte development and spermatogenesis. We established that the greater amberjack cultured along the southern coast of China reached sexual maturity at three years of age, and its reproductive season extended from February to April. Spawning of the cultured greater amberjack was successfully induced with a single injection of SdGnRHa/SdSN/DOM/HCG. Our findings indicate that similar to GnRHa, SNa is a potential stimulator of reproduction that can be used to artificially induce spawning in marine fish.
| S-EPMC9505948 | biostudies-literature
Project description:Greater amberjack (Seriola dumerili) is a new species in marine aquaculture with high mortalities at the larval stages. The microbiota of amberjack larvae was analyzed using 16S rDNA sequencing in two groups, one added copepod nauplii (Acartia tonsa) in the diet, and one without copepods (control). In addition, antagonistic bacteria were isolated from amberjack larvae and live food cultures. Proteobacteria was the most abundant phylum followed by Bacteroidota in amberjack larvae. The composition and diversity of the microbiota were influenced by age, but not by diet. Microbial community richness and diversity significantly increased over time. Rhodobacteraceae was the most dominant family followed by Vibrionaceae, which showed the highest relative abundance in larvae from the control group 31 days after hatching. Alcaligenes and Thalassobius genera exhibited a significantly higher relative abundance in the copepod group. Sixty-two antagonistic bacterial strains were isolated and screened for their ability to inhibit four fish pathogens (Aeromonas veronii, Vibrio harveyi, V. anguillarum, V. alginolyticus) using a double-layer test. Phaeobacter gallaeciensis, Phaeobacter sp., Ruegeria sp., and Rhodobacter sp. isolated from larvae and Artemia sp. inhibited the fish pathogens. These antagonistic bacteria could be used as host-derived probiotics to improve the growth and survival of the greater amberjack larvae.
| S-EPMC10456766 | biostudies-literature