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Tetraodon nigroviridis

ABSTRACT: freshwater pufferfish with highly compact vertebrate genome

PROVIDER: PRJNA12349 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	CAAE01.dat.gz	Other
	CAAE01.fasta.gz	Fasta.gz
	CAAE01.master.dat	Other
	SRR1183424.fastq.gz	Fastqsanger.gz

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Tetraodon nigroviridis

Project description:Genome sequencing of the spotted green pufferfish

| PRJNA20435 | ENA

Expression of known and predicted genes in tissues of Tetraodon nigroviridis (pufferfish)

Project description:Expression of known and predicted genes in tissues of Tetraodon nigroviridis (pufferfish) pooled from multiple healthy individuals.

2009-04-16 | GSE12976 | GEO

Tetraodon nigroviridis

Project description:Expression of known and predicted genes in tissues of Tetraodon nigroviridis (pufferfish)

| PRJNA112587 | ENA

Expression of known and predicted genes in tissues of Tetraodon nigroviridis (pufferfish)

Project description:Expression of known and predicted genes in tissues of Tetraodon nigroviridis (pufferfish) pooled from multiple healthy individuals. Two-colour experiments with two different tissues hybridized to each array. Each tissue is arrayed in replicate with dye swaps. Tissues: Beak, Brain, Calvaria, Connective tissue, Eye, Fin, Gallbladder, Gill, Heart, Intestine, Kidney, Liver, Ovary, Red muscle, Skin, Spleen, Stomach, Swimbladder, Testis, White muscle

2010-06-19 | E-GEOD-12976 | biostudies-arrayexpress

Tetraodon nigroviridis

Project description:Tetraodon nigroviridis

| PRJNA12350 | ENA

Tetraodon nigroviridis

Project description:Tetraodon nigroviridis miRNA profiling upon stimulation of IFN-gamma

| PRJNA239961 | ENA

Tetraodon nigroviridis

Project description:Global gene expression analysis of green spotted puffer fish gills in response to environmental calcium changes

| PRJNA122129 | ENA

Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

Project description:BackgroundThe G-protein-coupled receptors (GPCRs) constitute one of the largest and most ancient superfamilies of membrane proteins. They play a central role in physiological processes affecting almost all aspects of the life cycle of an organism. Availability of the complete sets of putative members of a family from diverse species provides the basis for cross genome comparative studies.ResultsWe have defined the repertoire of GPCR superfamily of Tetraodon complement with the availability of complete sequence of the freshwater puffer fish Tetraodon nigroviridis. Almost all 466 Tetraodon GPCRs (Tnig-GPCRs) identified had a clear human homologue. 189 putative human and Tetraodon GPCR orthologous pairs could be identified. Tetraodon GPCRs are classified into five GRAFS families, by phylogenetic analysis, concurrent with human GPCR classification.ConclusionDirect comparison of GPCRs in Tetraodon and human genomes displays a high level of orthology and supports large-scale gene duplications in Tetraodon. Examples of lineage specific gene expansions were also observed in opsin and odorant receptors. The human and Tetraodon GPCR sequences are analogous in terms of GPCR subfamilies but display disproportionate numbers of receptors at the subfamily level. The teleost genome with its expanded set of GPCRs provides additional and interesting comparators to study both evolution and function of these receptors.

| S-EPMC1187884 | biostudies-literature

The Tetraodon Nigroviridis Transcriptome During Early Development.

Project description:Tetraodon embryos were obtained by in vitro fertilization of eggs and their development was observed through brightfield microscopy. The embryo development was divided into distinct stages using morphological features as described for normal development of other fish species like medaka (Oryzias latipes), zebrafish (Danio rerio), and fugu (Takifugu rubripes). Total RNA was extracted with Trizol (Invitrogen) according to the manufacturer s protocol from eggs, whole embryo at 30% epiboly (30 epi) and whole embryo at 24 hours post fertilisation (24 hpf). The RNA samples were treated with 2U Dnase I (Qiagen) per μg RNA sample at 37°C for 10 minutes. Digested samples were then treated with 20 mg/mL proteinase K (Sigma Aldrich) at 37°C for 45 minutes. The quality and quantity of total RNA were assessed with the Bioanalyzer 2100 (Agilent) and no sign of degradation was detected (RIN > 9.0). Sequencing libraries were generated from total RNA samples following the Truseq RNA protocol (Illumina). Single end reads (1 x 50 nucleotides) were obtained from 3 lanes on a Hiseq1000 using SBS v3 kits (Illumina).

2016-07-28 | E-MTAB-3804 | biostudies-arrayexpress

Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis.

Project description:Tetraodon nigroviridis is a freshwater pufferfish 20-30 million years distant from Fugu rubripes. The genome of both tetraodontiforms is compact, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes. The previously uncharacterized Tetraodon genome is described here together with a detailed analysis of its repeat content and organization. We report the sequencing of 46 megabases of bacterial artificial chromosome (BAC) end sequences, which represents a random DNA sample equivalent to 13% of the genome. The sequence and location of rRNA gene clusters, centromeric and subtelocentric satellite sequences have been determined. Minisatellites and microsatellites have been cataloged and notable differences were observed in comparison with microsatellites from Fugu. The genome contains homologies to all known families of transposable elements, including Ty3-gypsy, Ty1-copia, Line retrotransposons, DNA transposons, and retroviruses, although their overall abundance is <1%. This structural analysis is an important prerequisite to sequencing the Tetraodon genome.

| S-EPMC310905 | biostudies-literature

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