ArticleBMC genomics2016
Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Integrative Methylome and Transcriptome Analysis of DNA Methylation and Sex-Biased Gene Expression in Northern Pike (Animals : an open access journal from MDPI · 2026Article
- Exploring the Effect of Whole-Genome Duplication on Salmonid LincRNA Repertoire.International journal of molecular sciences · 2026Article
- MiR-8159-x and miR-200-z induced liver injury of tsinling lenok trout through endoplasmic reticulum and mitochondria interaction under high-temperature stress.Fish physiology and biochemistry · 2026Article
- Circulating microRNAs reveal egg-brain crosstalk and a brain-predominant microRNA linked to the onset of the next reproductive cycle in iteroparous salmonids.BMC biology · 2026Article
- Micro-RNA expression data from common carp brain cells infected by Cyvirus cyprinidallo3 at permissive and non-permissive temperatures.Data in brief · 2025Article
- Sexual Antagonism and Sex Determination in Three Syngnathid Species Alongside a Male Pregnancy Gradient.Genome biology and evolution · 2025Article
- The Discovery and Characterization of Conserved and Novel miRNAs in the Different Developmental Stages and Organs of Pikeperch (International journal of molecular sciences · 2023Article
- microRNA regulation of skin pigmentation in golden-back mutant of crucian carp from a rice-fish integrated farming system.BMC genomics · 2023Article
- Deciphering sex-specific miRNAs as heat-recorders in zebrafish.Scientific reports · 2022Article
- Article
- Physical Enrichment Triggers Brain Plasticity and Influences Blood Plasma Circulating miRNA in Rainbow Trout (Biology · 2022Article
- Differentially Expressed miRNAs and mRNAs in Regenerated Scales of Rainbow Trout (Animals : an open access journal from MDPI · 2022Article
- Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome forBiology · 2022Article
- Circulating miRNA repertoire as a biomarker of metabolic and reproductive states in rainbow trout.BMC biology · 2021Article
- A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks.BMC genomics · 2021Article
- PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes.Frontiers in genetics · 2021Article
- Non-coding RNA Expression Patterns of Two Different Teleost Gonad Maturation Stages.Marine biotechnology (New York, N.Y.) · 2020Article
- Potential immune regulatory role of miR-146a upon Aeromonas hydrophila and Edwardsiella piscicida infections in zebrafish.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2020Article
- High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress.Frontiers in physiology · 2020Article
- High-throughput sequencing reveals microRNAs in response to heat stress in the head kidney of rainbow trout (Oncorhynchus mykiss).Functional & integrative genomics · 2019Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in a wide variety of physiological processes. They can control both temporal and spatial gene expression and are believed to regulate 30 to 70% of the genes. Data are however limited for fish species, with only 9 out of the 30,000 fish species present in miRBase. The aim of the current study was to discover and characterize rainbow trout (Oncorhynchus mykiss) miRNAs in a large number of tissues using next-generation sequencing in order to provide an extensive repertoire of rainbow trout miRNAs.
resultsA total of 38 different samples corresponding to 16 different tissues or organs were individually sequenced and analyzed independently in order to identify a large number of miRNAs with high confidence. This led to the identification of 2946 miRNA loci in the rainbow trout genome, including 445 already known miRNAs. Differential expression analysis was performed in order to identify miRNAs exhibiting specific or preferential expression among the 16 analyzed tissues. In most cases, miRNAs exhibit a specific pattern of expression in only a few tissues. The expression data from sRNA sequencing were confirmed by RT-qPCR. In addition, novel miRNAs are described in rainbow trout that had not been previously reported in other species.
conclusionThis study represents the first characterization of rainbow trout miRNA transcriptome from a wide variety of tissue and sets an extensive repertoire of rainbow trout miRNAs. It provides a starting point for future studies aimed at understanding the roles of miRNAs in major physiological process such as growth, reproduction or adaptation to stress. These rainbow trout miRNAs repertoire provide a novel resource to advance genomic research in salmonid species.
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