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: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:BackgroundFish 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%.ResultsThis 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.ConclusionsOverall, 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: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: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: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: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:Butylparaben (BuP), as an emerging contaminant with endocrine-disrupting effects, may exert effects on skin pigmentation in fish by interfering with the neuroendocrine system. Therefore, models of BuP exposure in Nile tilapia (Oreochromis niloticus) were established by adding different doses of BuP (0, 5, 50, 500, and 5000 ng/L) for 56 days. The obtained results showed that BuP exposure induced darker skin pigmentation, manifested as increased melanin content of skin, while genes related to melanin synthesis, including α-MSH and Asip2, significantly changed. In addition, BuP exposure reduced dopamine and γ-aminobutyric acid content in the brain, which is related to the synthesis of α-MSH. Furthermore, the release of neurotransmitters from the brain is affected by light. Thus, the relative gene expression levels in the phototransduction pathway were evaluated to explore the molecular mechanism of BuP-induced darker skin pigmentation, and the obtained results showed that Arr3a and Arr3b expression was significantly upregulated, whereas Opsin expression was significantly downregulated in a BuP dose-dependent manner, indicating that BuP inhibited phototransduction from the retina to the brain. Importantly, correlation analysis results showed that all melanin indexes were significantly positively correlated with Arr3b expression and negatively correlated with Opsin expression. This study indicated that BuP induced darker skin pigmentation in Nile tilapia via the neuroendocrine circuit, which reveals the underlying molecular mechanism for the effects of contaminants in aquatic environments on skin pigmentation in fish.
| S-EPMC9959106 | biostudies-literature
Project description:Kisspeptin has recently been recognized as a critical regulator of reproductive function in vertebrates. During the sexual development, kisspeptin neurons receive sex steroids feedback to trigger gonadotropin-releasing hormone (GnRH) neurons. In teleosts, a positive correlation has been found between the thyroid status and the reproductive status. However, the role of thyroid hormone in the regulation of kisspeptin system remains unknown. We cloned and characterized a gene encoding kisspeptin (kiss2) in a cichlid fish, the Nile tilapia (Oreochromis niloticus). Expression of kiss2 mRNA in the brain was analyzed by in situ hybridization. The effect of thyroid hormone (triiodothyronine, T3) and hypothyroidism with methimazole (MMI) on kiss2 and the three GnRH types (gnrh1, gnrh2, and gnrh3) mRNA expression was analyzed by real-time PCR. Expression of thyroid hormone receptor mRNAs were analyzed in laser-captured kisspeptin and GnRH neurons by RT-PCR. The kiss2 mRNA expressing cells were seen in the nucleus of the lateral recess in the hypothalamus. Intraperitoneal administration of T3 (5 μg/g body weight) to sexually mature male tilapia significantly increased kiss2 and gnrh1 mRNA levels at 24 h post injection (P < 0.001), while the treatment with an anti-thyroid, MMI (100 ppm for 6 days) significantly reduced kiss2 and gnrh1 mRNA levels (P < 0.05). gnrh2, gnrh3, and thyrotropin-releasing hormone mRNA levels were insensitive to the thyroid hormone manipulations. Furthermore, RT-PCR showed expression of thyroid hormone receptor mRNAs in laser-captured GnRH neurons but not in kiss2 neurons. This study shows that GnRH1 may be directly regulated through thyroid hormone, while the regulation of Kiss2 by T3 is more likely to be indirect.
| S-EPMC3839095 | 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