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Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication

ABSTRACT: Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication

PROVIDER: PRJNA560184 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9965150_1.fastq.gz	Fastqsanger.gz
	SRR9965150_2.fastq.gz	Fastqsanger.gz
	SRR9965151_1.fastq.gz	Fastqsanger.gz
	SRR9965151_2.fastq.gz	Fastqsanger.gz
	SRR9965152_1.fastq.gz	Fastqsanger.gz

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Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication

Project description:Background: The historically recent domestication of fishes has been essential for mankind due to the overexploitation of natural stocks and the increasing protein demand to meet the needs of a growing human population. Selection for relevant traits, such as growth, during domestication is a complex process whose epigenetic basis is poorly understood. Results: We have determined changes that occur in the muscle transcriptome after a single generation of Nile tilapia (Oreochromis niloticus) domestication. There was a downregulation of 2015 genes in fish reared in captivity compared to their wild progenitors. In contrast, several myogenic and metabolic genes that can affect growth potential were upregulated. Methods: RNA was extracted and ribosomal RNA was removed using the Ribo-Zero gold rRNA removal kit. RNA libraries were prepared using the NEBNext Ultra II directional RNA library prep kit for Illumina. In total, we obtained 480 million 150 bp paired-end reads. Conclusion: Taken together, our data indicate that thousands of genes were differentially expressed within a single generation of fish domestication.

2020-02-21 | GSE135811 | GEO

Tilapia cultivar:Nile tilapia

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Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication.

Project description:The historically recent domestication of fishes has been essential to meet the protein demands of a growing human population. Selection for traits of interest during domestication is a complex process whose epigenetic basis is poorly understood. Cytosine hydroxymethylation is increasingly recognized as an important DNA modification involved in epigenetic regulation. In the present study, we investigated if hydroxymethylation plays a role in fish domestication and demonstrated for the first time at a genome-wide level and single nucleotide resolution that the muscle hydroxymethylome changes after a single generation of Nile tilapia (Oreochromis niloticus, Linnaeus) domestication. The overall decrease in hydroxymethylcytosine levels was accompanied by the downregulation of 2015 genes in fish reared in captivity compared to their wild progenitors. In contrast, several myogenic and metabolic genes that can affect growth potential were upregulated. There were 126 differentially hydroxymethylated cytosines between groups, which were not due to genetic variation; they were associated with genes involved in immune-, growth- and neuronal-related pathways. Taken together, our data unveil a new role for DNA hydroxymethylation in epigenetic regulation of fish domestication with impact in aquaculture and implications in artificial selection, environmental adaptation and genome evolution.

| S-EPMC7116051 | biostudies-literature

Global DNA methylation changes in Nile tilapia gonad during high-temperature induced masculinization

Project description:In fish, the sex determining mechanisms can broadly be classified as genotypic (GSD), temperature-dependent (TSD), or genotypic plus temperature effects (GSD+TE). For the fish species with TSD or GSD+TE, extremely high or low temperature can affect its sex determination and differentiation. For long time, the underlying changes in DNA methylation that occur during high or low temperature induced sex reversal have not been fully clarified. In this study, we used Nile tilapia as a model to perform a genome-wide survey of differences in DNA methylation in female and male gonads between control and high temperature induced groups using methylated DNA immunoprecipitation (MeDIP). We identified the high temperature induction-related differentially methylated regions (DMRs), and performed functional enrichment analysis for genes exhibiting DMR. These identified differentially methylated genes were potentially involved in the connection between environmental temperature and sex reversal in Nile tilapia. In this study, four samples (control females, CF; control males, CM; induced females, IF; induced males, IM) were analyzed.

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Global DNA methylation changes in Nile tilapia gonad during high-temperature induced masculinization

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Project description:Nile Tilapia GIFT genome assembly

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Project description:A novel sex-determining QTL in Nile tilapia (Oreochromis niloticus).

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