Abbassa (GIANT) Nile Tilapia (Oreochromis niloticus abbassa) genome assembly and annotation ORENIAB8128_EIv1.0
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB57170 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| Other | ||||
| ERR10448959.fastq.gz | Fastqsanger.gz | |||
| ERR10448960.fastq.gz | Fastqsanger.gz | |||
| ERR10448962_1.fastq.gz | Fastqsanger.gz |
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Project description:Fingerlings of Oreochromis niloticus collected in an artificial urban lake from Belo Horizonte, Minas Gerais, Brazil, were evaluated for natural infection with trematodes. Morphological taxonomic identification of four fluke species was performed in O. niloticus examined, and the total prevalence of metacercariae was 60.7% (37/61). Centrocestus formosanus, a heterophyid found in the gills, was the species with the highest prevalence and mean intensity of infection (31.1% and 3.42 (1-42), resp.), followed by the diplostomid Austrodiplostomum compactum (29.5% and 1.27 (1-2)) recovered from the eyes. Metacercariae of Drepanocephalus sp. and Ribeiroia sp., both found in the oral cavity of the fish, were verified at low prevalences (8.2% and 1.6%, resp.) and intensities of infection (only one metacercaria of each of these species per fish). These species of trematodes are reported for the first time in O. niloticus from South America. The potential of occurrence of these parasites in tilapia farming and the control strategies are briefly discussed.
| S-EPMC4251074 | biostudies-other
Project description:BACKGROUND:Fish species often exhibit significant sexual dimorphism for commercially important traits. Accordingly, the control of phenotypic sex, and in particular the production of monosex cultures, is of particular interest to the aquaculture industry. Sex determination in the widely farmed Nile tilapia (Oreochromis niloticus) is complex, involving genomic regions on at least three chromosomes (chromosomes 1, 3 and 23) and interacting in certain cases with elevated early rearing temperature as well. Thus, sex ratios may vary substantially from 50%. RESULTS:This study focused on mapping sex-determining quantitative trait loci (QTL) in families with skewed sex ratios. These included four families that showed an excess of males (male ratio varied between 64% and 93%) when reared at standard temperature (28°C) and a fifth family in which an excess of males (96%) was observed when fry were reared at 36°C for ten days from first feeding. All the samples used in the current study were genotyped for two single-nucleotide polymorphisms (rs397507167 and rs397507165) located in the expected major sex-determining region in linkage group 1 (LG 1). The only misassigned individuals were phenotypic males with the expected female genotype, suggesting that those offspring had undergone sex-reversal with respect to the major sex-determining locus. We mapped SNPs identified from double digest Restriction-site Associated DNA (ddRAD) sequencing in these five families. Three genetic maps were constructed consisting of 641, 175 and 1,155 SNPs from the three largest families. QTL analyses provided evidence for a novel genome-wide significant QTL in LG 20. Evidence was also found for another sex-determining QTL in the fifth family, in the proximal region of LG 1. CONCLUSIONS:Overall, the results from this study suggest that these previously undetected QTLs are involved in sex determination in the Nile tilapia, causing sex reversal (masculinisation) with respect to the XX genotype at the major sex-determining locus in LG 1.
| S-EPMC4358704 | biostudies-literature
Project description:Nile tilapia (Oreochromis niloticus) is a globally significant aquaculture species rapidly gaining status as a farmed commodity. In West Africa, wild Nile tilapia genetic resources are abundant yet knowledge of fine-scale population structure and patterns of natural genetic variation are limited. Coinciding with this is a burgeoning growth in tilapia aquaculture in Ghana and other countries within the region underpinned by locally available genetic resources. Using 192 single nucleotide polymorphism (SNP) markers this study conducted a genetic survey of Nile tilapia throughout West Africa, sampling 23 wild populations across eight countries (Benin, Burkina Faso, Côte d'Ivoire, Ghana, Togo, Mali, Gambia and Senegal), representing the major catchments of the Volta, Niger, Senegal and Gambia River basins. A pattern of isolation-by-distance and significant spatial genetic structure was identified throughout West Africa (Global FST = 0.144), which largely corresponds to major river basins and, to a lesser extent, sub-basins. Two populations from the Gambia River (Kudang and Walekounda), one from the western Niger River (Lake Sélingué) and one from the upper Red Volta River (Kongoussi) showed markedly lower levels of diversity and high genetic differentiation compared to all other populations, suggesting genetically isolated populations occurring across the region. Genetic structure within the Volta Basin did not always follow the pattern expected for sub-river basins. This study identifies clear genetic structuring and differentiation amongst West African Nile tilapia populations, which concur with broad patterns found in previous studies. In addition, we provide new evidence for fine-scale genetic structuring within the Volta Basin and previously unidentified genetic differences of populations in Gambia. The 192 SNP marker suite used in this study is a useful tool for differentiating tilapia populations and we recommend incorporating this marker suite into future population screening of O. niloticus. Our results form the basis of a solid platform for future research on wild tilapia genetic resources in West Africa, and the identification of potentially valuable germplasm for use in ongoing breeding programs for aquaculture.
| S-EPMC6856548 | biostudies-literature
Project description:This is the first report of outbreaks of Streptococcus iniae in Nile tilapia farms in South America. Seven isolates were identified by biochemical, serological and molecular tests. Their 16S rRNA gene sequences showed 100% similarity with S. iniae ATCC 29178 and two distinct PFGE patterns were observed for Brazilian isolates.
| S-EPMC3768829 | biostudies-literature
Project description:TSP1 was reported to be involved in multiple biological processes including the activation of TGF-β signaling pathways and the regulation of angiogenesis during wound repair and tumor growth, while its role in ovarian folliculogenesis remains to be elucidated. In the present study, Tsp1a was found to be expressed in the oogonia and granulosa cells of phase I to phase IV follicles in the ovaries of Nile tilapia by immunofluorescence. tsp1a homozygous mutants were generated by CRISPR/Cas9. Mutation of tsp1a resulted in increased oogonia, reduced secondary growth follicles and delayed ovary development. Expression of the cell proliferation marker PCNA was significantly up-regulated in the oogonia of the mutant ovaries. Furthermore, transcriptomic analysis revealed that expressions of DNA replication related genes were significantly up-regulated, while cAMP and MAPK signaling pathway genes which inhibit cell proliferation and promote cell differentiation were significantly down-regulated. In addition, aromatase (Cyp19a1a) expression and serum 17β-estradiol (E2) concentration were significantly decreased in the mutants. These results indicated that lacking tsp1a resulted in increased proliferation and inhibited differentiation of oogonia, which in turn, resulted in increased oogonia, reduced secondary growth follicles and decreased E2. Taken together, our results indicated that tsp1a was essential for ovarian folliculogenesis in Nile tilapia.
| S-EPMC7460569 | biostudies-literature
Project description:Since its discovery in 2014, tilapia lake virus (TiLV) has emerged as a significant cause of mortality in tilapia cultured in Asia, Africa, and South America. Here, we report the complete genome sequence of a TiLV isolate obtained during a diagnostic investigation of an ongoing mortality event involving Nile tilapia cultured in Thailand.
| S-EPMC6025939 | biostudies-literature
Project description:C-reactive protein (CRP) is an acute-phase protein that can be used as an early diagnostic marker for inflammation, which is also an evolutionarily conserved protein and has been identified from arthropods to mammals. However, the roles of CRP during the immune response of Nile tilapia (Oreochromis niloticus) remain unclear. In this study, a CRP gene from Nile tilapia (On-CRP) was identified, and its roles in response to bacterial infection were investigated in vivo or in vitro. On-CRP was found to contain an open reading frame of 675 bp, encoding a polypeptide of 224 amino acids with the conservative pentraxin domain. On-CRP shares more than 50% of its identity with other fish species, and 30% of its identity with mammals. The transcriptional level of On-CRP was most abundant in the liver and its transcripts can be remarkably induced following Streptococcus agalactiae and Aeromonas hydrophila infection. Furthermore, in vitro analysis indicated that the recombinant protein of On-CRP improved phagocytic activity of monocytes/macrophages, and possessed a bacterial agglutination activity in a calcium-dependent manner. Both in vivo and in vitro experiments indicated that On-CRP could promote inflammation and activate the complement pathway. However, a direct relationship between CRP and several immune pathways could not be confirmed. The present data lays a theoretical foundation to further explore the mechanism of how CRP protects fish against bacterial infection.
| S-EPMC9405397 | biostudies-literature
Project description:Nile tilapia (Oreochromis niloticus) is an African freshwater fish that displays a genetic sex determination system (XX|XY) where high temperatures (above 32°C to 36.5°C) induce masculinization. In Nile tilapia, the thermosensitive period was reported from 10 to 30 days post fertilization. In their natural environment, juveniles may encounter high temperatures that are above the optimal temperature for growth (27-30°C). The relevance of the thermal sex reversal mechanism in a natural context remains unclear. The main objective of our study is to determine whether sexually undifferentiated juveniles spontaneously prefer higher, unfavorable temperatures and whether this choice skews the sex ratio toward males. Five full-sib progenies (from 100% XX crosses) were subjected to (1) a horizontal three-compartment thermal step gradient (thermal continuum 28°C- 32°C- 36.5°C) during the thermosensitive period, (2) a control continuum (28°C- 28°C- 28°C) and (3) a thermal control tank (36.5°C). During the first days of the treatment, up to an average of 20% of the population preferred the masculinizing compartment of the thermal continuum (36.5°C) compared to the control continuum. During the second part of the treatment, juveniles preferred the lower, nonmasculinizing 32°C temperature. This short exposure to higher temperatures was sufficient to significantly skew the sex ratio toward males, compared to congeners raised at 28°C (from 5.0 ± 6.7% to 15.6 ± 16.5% of males). The proportion of males was significantly different in the thermal continuum, thermal control tank and control continuum, and it was positively correlated among populations. Our study shows for the first time that Nile tilapia juveniles can choose a masculinizing temperature during a short period of time. This preference is sufficient to induce sex reversal to males within a population. For the first time, behavior is reported as a potential player in the sex determination mechanism of this species.
| S-EPMC6375642 | biostudies-literature
Project description:Collagen plays an important role in the formation of extracellular matrix (ECM) and development/migration of cells and tissues. Here we report the preparation of collagen and collagen hydrogel from the skin of tilapia and an evaluation of their potential as a wound dressing for the treatment of refractory wounds. The acid-soluble collagen (ASC) and pepsin-soluble collagen (PSC) were extracted and characterized using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), differential scanning calorimetry (DSC), circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) analysis. Both ASC and PSC belong to type I collagen and have a complete triple helix structure, but PSC shows lower molecular weight and thermal stability, and has the inherent low antigenicity. Therefore, PSC was selected to prepare biomedical hydrogels using its self-aggregating properties. Rheological characterization showed that the mechanical strength of the hydrogels increased as the PSC content increased. Scanning electron microscope (SEM) analysis indicated that hydrogels could form a regular network structure at a suitable PSC content. Cytotoxicity experiments confirmed that hydrogels with different PSC content showed no significant toxicity to fibroblasts. Skin repair experiments and pathological analysis showed that the collagen hydrogels wound dressing could significantly accelerate the healing of deep second-degree burn wounds and the generation of new skin appendages, which can be used for treatment of various refractory wounds.
| S-EPMC7230254 | biostudies-literature
Project description:Aquatic animals are known for their myriad of beneficial bacteria with diverse biologically active compounds. The current study was aimed to isolate and characterize potentially beneficial lactic acid bacteria from Nile Tilapia and evaluate their pharmaceutical applications. The fish samples were dissected and stomach, intestine, and gills were collected and serially diluted for the isolation of lactic acid bacteria (LAB) on BCP agar media. Identification of isolate was carried by biochemical and molecular characterization using API kit and 16S rRNA gene sequencing analysis, respectively. Further, KS-TN11 was assessed for α-glucosidase inhibitory potential using the chromogenic method. A lactic acid bacterium KS-TN11 was isolated from the stomach of Nile Tilapia and identified as Leuconostoc mesenteroides. Effect of KS-TN11 on lipid accumulation in adipocytes was done by using Oil Red O staining. The isolate showed strong antibacterial activity against a number of pathogenic bacteria in vitro. In addition, L. mesenteroides KS-TN11 KS-TN11 (50 mg/ml and 100 mg/ml) tends to inhibit adipogenesis in 3T3-L1 adipocytes and thus may have possible anti-obesity effects. Moreover, L. mesenteroides KS-TN11 exhibited substantial α-glucosidase inhibitory activities by 41.33% at 50 mg/ml and 64% at 100 mg/ml, respectively. The bacterium showed potent antibacterial activity against a number of pathogenic bacteria; in addition to alpha-glucosidase activity, and inhibition of lipid accumulation in 3T3-L1 cell line. These results reinforce KS-TN11 as a novel bacterium with an impending pharmaceutical application.
| S-EPMC5961753 | biostudies-literature