Dataset Information

Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance.

ABSTRACT: The mechanisms underlying the fast genome evolution that occurs during animal domestication are poorly understood. Here, we present a genome-wide epigenetic dataset that quantifies DNA hydroxymethylation at single nucleotide resolution among full-sib Nile tilapia (Oreochromis niloticus) with distinct growth performance. In total, we obtained 355 million, 75 bp reads from 5 large- and 5 small-sized fish on an Illumina NextSeq500 platform. We identified several growth-related genes to be differentially hydroxymethylated, especially within gene bodies and promoters. Previously, we proposed that DNA hydroxymethylation greatly affects the earliest responses to adaptation and potentially drives genome evolution through its targeted enrichment and elevated nucleotide transversion rates. This dataset can be analysed in various contexts (e.g., epigenetics, evolution and growth) and compared to other epigenomic datasets in the future, namely DNA methylation and histone modifications. With forthcoming advancements in genome research, this hydroxymethylation dataset will also contribute to better understand the epigenetic regulation of key genomic features, such as cis-regulatory and transposable elements.

SUBMITTER: Konstantinidis I

PROVIDER: S-EPMC9977925 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance.

Konstantinidis Ioannis I Sætrom Pål P Fernandes Jorge M O JMO

Scientific data 20230301 1

The mechanisms underlying the fast genome evolution that occurs during animal domestication are poorly understood. Here, we present a genome-wide epigenetic dataset that quantifies DNA hydroxymethylation at single nucleotide resolution among full-sib Nile tilapia (Oreochromis niloticus) with distinct growth performance. In total, we obtained 355 million, 75 bp reads from 5 large- and 5 small-sized fish on an Illumina NextSeq500 platform. We identified several growth-related genes to be different ...[more]

PMID: 36859394

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Project description:Selenium is an important micronutrient that has antioxidant, growth potential, and reproduction enhancement abilities in various organisms. The aquaculture industry is a significant contributor towards meeting the dietary requirements of a majority of the global population, which further warrants developing novel approaches for enhancing the production of dietary fish. This study was performed to assess the growth performance of Nile tilapia (Oreochromis niloticus) fingerlings (1 gm in average weight and 2.75 cm in average length) upon nano-selenium (Se-Nps) supplementation. Nanoselenium was synthesized using high-energy ball milling (HEBM) using a 10-hour dry milling technique at 10:1 ball-to-powder ratio (BPR), size characterized by XRD and TEM, followed by mixing with basal feed in desired concentrations (0.5 mg/kg, 1 mg/kg, and 2 mg/kg) and administration to Nile tilapia fingerlings for 30 days, followed by the evaluation of growth performance parameters, fatty acid profile analysis using GC-MS, and nutritional quality index (NQI): [Thrombogenicity Index (IT), Atherogenicity Index (IA), n-3/n-6, n-6/n-3)]. Nile tilapia supplemented with 1 mg/kg Se-Nps showed improved growth performance (RGR: 1576.04%, SGR: 4.70%, and FCR: 1.91), demonstrated by higher survivability (> 95%), isometric growth (coefficient of allometry, b = 2.81), and higher weight gain compared to control (RGR: 680.41%, SGR: 3.42%, and FCR: 1.31), 0.5 mg/kg Se-Nps (RGR: 770.83%, SGR: 3.61%, and FCR: 1.18) and 2 mg/kg Se-Nps (RGR: 383.67%, SGR: 2.63%, and FCR: 1.22). The average length-weight relationship assessed as the condition factor (K) was highest in the 1 mg/kg Se-Nps group compared to others (p < 0.05). GC-MS analysis revealed that Nile tilapia supplemented with 1 mg/kg Se-Nps showed better meat quality, higher amount of n-3 fatty acids, eicosapentaenoic acid, and docosahexaenoic acid, high PUFA/SAFA ratios (1.35) and n-3/n-6 (0.33) ratios, with low atherogenicity index (0.36) and thrombogenic index (0.44), and relatively low n-6/n-3 fatty acid ratio (3.00) compared to other groups. Overall, Se-Nps supplementation at 1 mg/kg enhanced the growth performance and meat quality in Nile tilapia, and therefore could be a potential growth-promoting micronutrient for aquaculture enhancement.

Project description:The aim of this study was to explore for the first time in omnivorous fish the concept of nutritional programming. A nutritional stimulus was accomplished by microinjecting 2 M glucose into yolk reserves during the alevin stage in Nile tilapia (Oreochromis niloticus). At the molecular level in fry, at 1 week post-injection, glucose stimuli were associated with the up-regulation of genes involved in glycolysis (pklr, hk1, hk2, and pkma), glucose transport (glut4) pathways and down-regulation of genes related to gluconeogenesis (g6pca1, g6pca2, and pck1) and amino acid catabolism (asat, alat) (P < 0.05), demonstrating that the larvae well received the glucose stimulus at a molecular level. Moreover, 20 weeks after glucose injection, early glucose stimuli were always linked to permanent effects in juvenile fish, as reflected by a higher level of glycolytic enzymes [gck, hk1 and hk2 at both mRNA and enzymatic levels and pyruvate kinase (PK) activity]. Finally, the effects of the glucose stimulus history were also examined in fish fed with two different dietary carbohydrate/protein levels (medium-carbohydrate diet, CHO-M; high-carbohydrate diet, CHO-H) in juvenile fish (during weeks 20-24). As expected, the CHO-H diet induced the expression of glycolytic and lipogenic genes (gck, pklr, hk1, hk2, fpkma, fasn, and g6pd) and suppressed the expression of gluconeogenic and amino acid catabolism genes (g6pca1, pck1, pck2, asat, alat, and gdh). Nevertheless, the early glucose stimulus led to persistent up-regulation of glycolytic enzymes (gck, pklr, hk1, and hk2) at both the mRNA and enzyme activity levels and glucose transporter glut4 as well as lower gluconeogenic pck1 gene expression (P < 0.05). More interestingly, the early glucose stimulus was associated with a better growth performance of juvenile fish irrespective of the diets. These permanent changes were associated with DNA hypomethylation in the liver and muscles, suggesting the existence of epigenetic mechanisms at the origin of programming. In conclusion, for the first time in tilapia, early glucose stimuli were found to be clearly associated with a positive metabolic programming effect later in life, improving the growth performance of the fish.

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Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance.

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Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance.

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