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Oreochromis niloticus

ABSTRACT: Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts

PROVIDER: PRJNA265129 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1634037.fastq.gz	Fastqsanger.gz

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Total RNA sequencing of the liver tissues of Oreochromis niloticus (Nile Tilapia) and of Pundamilia nyerei

Project description:Cichlids fishes exhibit extensive phenotypic diversification and speciation. In this study we integrate transcriptomic and proteomic signatures from two cichlids species, identify novel open reading frames (nORFs) and perform evolutionary analysis on these nORF regions. We embark comparative transrcriptomics and proteogenomic analysis of two metabolically active tissues, the testes and liver, of two cichlid species Oreochromis niloticus (Nile tilapia, ON) and Pundamilia nyererei (Makobe Island, PN). Our results suggest that the time scale of speciation of the two species can be better explained by the evolutionary divergence of these nORF genomic regions.

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Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts

Project description:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin-immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has only been used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genome-wide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation. examination of H3K4me3 in adult fin tissue of the Nile tilapia (Oreochromis niloticus)

2015-07-07 | E-GEOD-62791 | biostudies-arrayexpress

Metacercarial infection of wild Nile tilapia (Oreochromis niloticus) from Brazil.

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.

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Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts

2015-07-07 | GSE62791 | GEO

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