Marine medaka (Oryzias melastigma) gill
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA702883 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13758749.fastq.gz | Fastqsanger.gz | |||
| SRR13758750.fastq.gz | Fastqsanger.gz | |||
| SRR13758751.fastq.gz | Fastqsanger.gz | |||
| SRR13758752.fastq.gz | Fastqsanger.gz | |||
| SRR13758972.fastq.gz | Fastqsanger.gz |
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Project description:Hypoxia is amongst the most widespread and pressing problems in aquatic environments. For the first time, we demonstrate that fish (Oryzias melastigma) exposed to hypoxia show reproductive impairments in F2 generations despite these progenies (and their germ cells) having never been exposed to hypoxia. We further show that the observed transgenerational reproductive impairments are associated with a differential methylation pattern of specific genes in sperm of both F0 and F2.
2016-05-11 | GSE81312 | GEO
Project description:We performed miRNA transcriptome analysis of mature medaka tissues using high-throughput next generation sequencing technology. The small RNA libraries were contructed from brain, liver and gonads in mature male and female medaka and a total of more than 128 million sequencing reads were generated from the six small RNA libraries. By comparison to known miRNA database, a total of 223 known miRNA types were identified with more than 50% expressed in brain. The expression profiling showed that almost half of the miRNAs are tissue-specific, with only 55 miRNA types from 34 families common to all tissues. A small number of miRNAs are also gender-specific. The experimental validation was performed for five represented miRNA candidates and four of them are confirmed.
2014-07-01 | GSE42696 | GEO
Project description:BackgroundThe marine medaka Oryzias melastigma has been demonstrated as a novel model for marine ecotoxicological studies. However, the lack of genome and transcriptome reference has largely restricted the use of O. melastigma in the assessment of in vivo molecular responses to environmental stresses and the analysis of biological toxicity in the marine environment. Although O. melastigma is believed to be phylogenetically closely related to Oryzias latipes, the divergence between these two species is still largely unknown. Using Illumina high-throughput RNA sequencing followed by de novo assembly and comprehensive gene annotation, we provided transcriptomic resources for the brain, liver, ovary and testis of O. melastigma. We also investigated the possible extent of divergence between O. melastigma and O. latipes at the transcriptome level.ResultsMore than 14,000 transcripts across brain, liver, ovary and testis in marine medaka were annotated, of which 5880 transcripts were orthologous between O. melastigma and O. latipes. Tissue-enriched genes were identified in O. melastigma, and Gene Ontology analysis demonstrated the functional specificity of the annotated genes in respective tissue. Lastly, the identification of marine medaka-enriched transcripts suggested the necessity of generating transcriptome dataset of O. melastigma.ConclusionsOrthologous transcripts between O. melastigma and O. latipes, tissue-enriched genes and O. melastigma-enriched transcripts were identified. Genome-wide expression studies of marine medaka require an assembled transcriptome, and this sequencing effort has generated a valuable resource of coding DNA for a non-model species. This transcriptome resource will aid future studies assessing in vivo molecular responses to environmental stresses and those analyzing biological toxicity in the marine environment.
| S-EPMC4352242 | biostudies-literature
Project description:Iron (Fe) is an essential trace element for marine fish. However, our knowledge of Fe requirements at different development stages of marine fish is still limited. Here, we reported the efficient Fe absorption strategies adopted by larval fish under different dietary Fe supplementary levels (i.e., 0-640 mg/kg). Biokinetically, the larval fish controlled their dietary Fe assimilation efficiency (AE, 1.6-18.5%), and enhanced their waterborne Fe uptake (ca. 2.5 fold change of uptake rate constant) once the dietary Fe was deficient (i.e., 27.4 mg Fe/kg feed). Transcriptionally, the expression of hepcidin1 (hep1; Fe regulator; i.e., 2.3-15.7 fold change) in larval fish was positively correlated with the Fe supplementary levels. Comparatively, the female adult fish were poor in assimilating the added Fe source (i.e., ferric form) with similar life-sustainable levels of Fe (i.e., 0.046-0.12 μg/g/d assimilated for Fe supplementary levels of 27.4, 162 and 657 mg Fe/kg feed). The overall feeding experiments suggested that dietary net Fe flux sufficient for the normal growth of larval medaka was 0.71-1.75 μg/g/d (i.e., 83.9 mg Fe/kg feed), consistent with the modeled value (i.e., 1.09-2.16 μg/g/d). In female adults, the estimated essential net Fe flux was 0.88-0.90 μg/g/d.
| S-EPMC4877592 | biostudies-literature
Project description:Marine medaka Whole Transcriptome analysis
| PRJNA268138 | ENA
Project description:BackgroundMarine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters.ResultsIn this study, we reported a high-quality and accurate de novo genome assembly of marine medaka through the integration of single-molecule sequencing, Illumina paired-end sequencing, and 10X Genomics linked-reads. The 844.17 Mb assembly is estimated to cover more than 98% of the genome and is more continuous with fewer gaps and errors than the previous genome assembly. Comparison of O. melastigma with closely related species showed significant expansion of gene families associated with DNA repair and ATP-binding cassette (ABC) transporter pathways. We identified 274 genes that appear to be under significant positive selection and are involved in DNA repair, cellular transportation processes, conservation and stability of the genome. The positive selection of genes and the considerable expansion in gene numbers, especially related to stimulus responses provide strong supports for adaptations of O. melastigma under varying environmental stresses.ConclusionsThe highly contiguous marine medaka genome and comparative genomic analyses will increase our understanding of the underlying mechanisms related to its extraordinary adaptation capability, leading towards acceleration in the ongoing and future investigations in marine ecotoxicology.
| S-EPMC7493909 | biostudies-literature
Project description:Medaka gill filaments contain stem cells in their most apical domains and differentiated cells of diverse lineages in central and basal domains. We aim at identifying differentially expressed genes among these two functionally different regions.
2019-05-29 | GSE130939 | GEO
Project description:MeDIP on the marine medaka sperm (Oryzias melastigma)
| PRJNA321309 | ENA
Project description:Effects of hypoxia on brain proteome of marine medaka
| PRJNA672214 | ENA
Project description:Hypoxia causes gender-specfic hepatic toxicity in marine medaka
| PRJNA578030 | ENA