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EXAMPLES:

gene XLOC_000007
f7
RNA TCONS_00000019
bioproject PRJEB12982


  •   bowfin
    (Amia calva)
  •   eurasian perch
    (Perca fluviatilis)
  •   grass carp
    (Ctenopharyngodon idella)
  •   mexican tetra
    (Astyanax mexicanus)
  •   rainbow trout
    (Oncorhynchus mykiss)
  •   striped catfish
    (Pangasianodon hypophthalmus)
  •   tiger barb
    (Puntius tetrazona)
  •   zebrafish
    (Danio rerio)
  • simplified version

  •   bowfin
    (Amia calva)
  •   eurasian perch
    (Perca fluviatilis)
  •   grass carp
    (Ctenopharyngodon idella)
  •   mexican tetra
    (Astyanax mexicanus)
  •   rainbow trout
    (Oncorhynchus mykiss)
  •   striped catfish
    (Pangasianodon hypophthalmus)
  •   tiger barb
    (Puntius tetrazona)
  •   zebrafish
    (Danio rerio)
  • simplified version

Bioproject

  • Please select the sample of bioproject for visualization of expression.
  • Click on the node of the fold tree to expand the information about the bioproject and sample.
  • Check the sample checkbox for sample selection.
  • baseline
    • PRJNA435500:
          Transcriptome assembly data for Oncorhynchus mykiss red blood cells
      • key word
        • Baseline; rainbow trout; red blood cells; RNA-seq; de novo assembly; transcriptome; peptide fractionation; LC ESI-MSMS; proteome; functional network; immune response; CD-HIT; ERYTHROCYTES; PROTEIN; ANNOTATION; EXPRESSION; CYTOSCAPE
      • publication
        • Sara, P. M. , et al. "In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling." Genes 9.4(2018):1.
      • abstract
        • Nucleated red blood cells (RBCs) of fish have, in the last decade, been implicated in several immune-related functions, such as antiviral response, phagocytosis or cytokine-mediated signaling. RNA-sequencing (RNA-seq) and label-free shotgun proteomic analyses were carried out for in silico functional pathway profiling of rainbow trout RBCs. For RNA-seq, a de novo assembly was conducted, in order to create a transcriptome database for RBCs. For proteome profiling, we developed a proteomic method that combined: (a) fractionation into cytosolic and membrane fractions, (b) hemoglobin removal of the cytosolic fraction, (c) protein digestion, and (d) a novel step with pH reversed-phase peptide fractionation and final Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC ESI-MS/MS) analysis of each fraction. Combined transcriptome- and proteome- sequencing data identified, in silico, novel and striking immune functional networks for rainbow trout nucleated RBCs, which are mainly linked to innate and adaptive immunity. Functional pathways related to regulation of hematopoietic cell differentiation, antigen presentation via major histocompatibility complex class II (MHCII), leukocyte differentiation and regulation of leukocyte activation were identified. These preliminary findings further implicate nucleated RBCs in immune function, such as antigen presentation and leukocyte activation.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR9644930 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9645023 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9645024 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9645025 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9645026 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9645027 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9645028 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9645029 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9645030 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9644929 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9644931 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9644932 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9644934 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9644935 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9644936 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR6806638 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR6806639 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR6806642 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR8164499 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR8164502 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR8164496 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR8164498 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR6806637 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR6806641 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR8164503 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR9644933 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR8164501 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR7262889 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR7262891 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR7262892 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR7262893 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR7262894 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR6806640 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR8164500 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR7262890 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR8164497 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
          SRR6806636 Red blood cells from Oncorhynchus mykiss blood nan Red blood cells from Oncorhynchus mykiss nan
    • PRJNA389609:
          Rainbow trout RNA-seq from Swanson clonal line (13 tissues) and two tissues from pooled samples
      • key word
        • Baseline; [1]Co-expression network; LncRNA; LincRNA; Rainbow trout; CHROMATIN; ANNOTATION; REVEALS; PROTEIN; DIFFERENTIATION; QUANTIFICATION; TRANSCRIPTION; EVOLUTION; ALIGNMENT; [2]INTEGRATIVE ANNOTATION; GENE-REGULATION; EXPRESSION; EVOLUTION; DATABASE; TRANSCRIPTION; REVEALS; POPULATIONS; REPRESSION; INSIGHTS [3]3 ABUNDANCE CLASSES; RNA-SEQ DATA; ONCORHYNCHUS-MYKISS; MESSENGER-RNA; GENOME DUPLICATION; ATLANTIC SALMON; INTEGRATED MAP; FISH GENOMES; SKIN MUCUS; GENERATION
      • publication
        • [1]Wang J et al., "Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss).", Mar Biotechnol (NY), 2016 Apr;18(2):271-82; [2]Al-Tobasei R et al., "Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.", PLoS One, 2016;11(2):e0148940; [3]Salem M et al., "Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout.", PLoS One, 2015;10(3):e0121778
      • abstract
        • [1]Long noncoding RNAs (lncRNAs) have been recognized in recent years as key regulators of diverse cellular processes. Genome-wide large-scale projects have uncovered thousands of lncRNAs in many model organisms. Large intergenic noncoding RNAs (lincRNAs) are lncRNAs that are transcribed fromintergenic regions of genomes. To date, no lincRNAs in non-model teleost fish have been reported. Inthis report, we present the first reference catalog of 9674 rainbow trout lincRNAs based on analysis ofRNA-Seq data from 15 tissues. Systematic analysis revealed that lincRNAs in rainbow trout share many characteristics with those in other mammalian species. They are shorter and lower in exon number and expression level compared with protein-coding genes. They show tissue-specific expression pattern and are typically co-expressed with their neighboring genes. Co-expression network analysis suggested that many lincRNAs are associated with immune response, muscle differentiation, and neural development. The study provides an opportunity for future experimental and computational studies to uncover the functions of lincRNAs in rainbow trout. [2]The ENCODE project revealed that similar to 70% of the human genome is transcribed. While only 1-2% of the RNAs encode for proteins, the rest are non-coding RNAs. Long non-coding RNAs (lncRNAs) form a diverse class of non-coding RNAs that are longer than 200nt. Emerging evidence indicates that lncRNAs play critical roles in various cellular processes including regulation of gene expression. LncRNAs show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult. In this study, more than two billion Illumina sequence reads were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200nt, with more than 83-100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test. Depending on the filtering stringency conditions, between 31,195 and 54,503 lncRNAs were identified, with only 421 matching known lncRNAs in other species. A digital gene expression atlas revealed 2,935 tissue-specific and 3,269 ubiquitously-expressed lncRNAs. This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids. [3]Efforts to obtain a comprehensive genome sequence for rainbow trout are ongoing and will be complemented by transcriptome information that will enhance genome assembly and annotation. Previously, transcriptome reference sequences were reported using data from different sources. Although the previous work added a great wealth of sequences, a complete and well-annotated transcriptome is still needed. In addition, gene expression in different tissues was not completely addressed in the previous studies. In this study, non-normalized cDNA libraries were sequenced from 13 different tissues of a single doubled haploid rainbow trout from the same source used for the rainbow trout genome sequence. A total of similar to 1.167 billion paired-end reads were de novo assembled using the Trinity RNA-Seq assembler yielding 474,524 contigs > 500 base-pairs. Of them, 287,593 had homologies to the NCBI non-redundant protein database. The longest contig of each cluster was selected as a reference, yielding 44,990 representative contigs. A total of 4,146 contigs (9.2%), including 710 full-length sequences, did not match any mRNA sequences in the current rainbow trout genome reference. Mapping reads to the reference genome identified an additional 11,843 transcripts not annotated in the genome. A digital gene expression atlas revealed 7,678 housekeeping and 4,021 tissue-specific genes. Expression of about 16,000-32,000 genes (35-71% of the identified genes) accounted for basic and specialized functions of each tissue. White muscle and stomach had the least complex transcriptomes, with high percentages of their total mRNA contributed by a small number of genes. Brain, testis and intestine, in contrast, had complex transcriptomes, with a large numbers of genes involved in their expression patterns. This study provides comprehensive de novo transcriptome information that is suitable for functional and comparative genomics studies in rainbow trout, including annotation of the genome.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR5657602 P_Oocyte Oocyte nan Pooled nan
          SRR5657600 S_Brain Brain nan Swanson clonal line nan
          SRR5657599 S_HeadKidney Head kidney nan Swanson clonal line nan
          SRR5657595 S_RedMuscle Red muscle nan Swanson clonal line nan
          SRR5657598 S_Gill Gill nan Swanson clonal line nan
          SRR5657603 S_WhiteMuscle White muscle nan Swanson clonal line nan
          SRR5657604 P_Pineal Pineal gland nan Pooled nan
          SRR5657605 S_Stomach Stomach nan Swanson clonal line nan
          SRR5657597 S_Kidney Kidney nan Swanson clonal line nan
          SRR5657606 S_Testis Testis nan Swanson clonal line nan
          SRR5657593 S_Spleen Spleen nan Swanson clonal line nan
          SRR5657592 S_Skin Skin nan Swanson clonal line nan
          SRR5657594 S_Liver Liver nan Swanson clonal line nan
          SRR5657596 S_Intestine Intestine nan Swanson clonal line nan
          SRR5657601 S_Fat Fat nan Swanson clonal line nan
    • PRJNA657617:
          Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during critical early life stages (rainbow trout)
      • key word
        • Baseline, strain, high growth rates, immune performance, life stages
      • publication
        • nan
      • abstract
        • Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain is resistant to development of soy-induced enteritis, an inflammatory intestinal pathology that occurs often in high-value carnivorous aquaculture species. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the homeostatic intestinal gene expression of the select strain to that of a commercial control line of trout. Samples were collected at early life stages known to be critical in the development of host-microbe interactions in the gut of rainbow trout. All female cohorts of both strains were reared alongside starting from eggs. Intestinal samples from 5 fish per group (2 fish strains; 2 developmental stages; 20 samples total) were used to generate mRNA selected stranded RNA-seq libraries for high throughput sequencing. Reads were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the two strains of trout and the developmental stages. Overall design: An all-female cohort of the select and commercial strains of rainbow trout were reared in flow-through spring water (15°C) starting from eggs. From first feeding to the conclusion of the experiment, both strains received a commercial trout starter diet. Intestinal samples were collected from both groups after ten days of feeding which occurred at 20 days post hatch (dph), and at 65 dph, which is just prior to the time when we traditionally switch the fish to an all plant protein diet. RNAseq libraries were prepared for five intestinal samples per experimental group for a total of 20 samples.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR12463372 GSM4729700 intestine nan Commercial Strain 20dph Biological Rep1 nan
          SRR12463373 GSM4729701 intestine nan Commercial Strain 20dph Biological Rep2 nan
          SRR12463374 GSM4729702 intestine nan Commercial Strain 20dph Biological Rep3 nan
          SRR12463375 GSM4729703 intestine nan Commercial Strain 20dph Biological Rep4 nan
          SRR12463376 GSM4729704 intestine nan Commercial Strain 20dph Biological Rep5 nan
          SRR12463377 GSM4729705 intestine nan Select Strain 20dph Biological Rep1 nan
          SRR12463378 GSM4729706 intestine nan Select Strain 20dph Biological Rep2 nan
          SRR12463379 GSM4729707 intestine nan Select Strain 20dph Biological Rep3 nan
          SRR12463380 GSM4729708 intestine nan Select Strain 20dph Biological Rep4 nan
          SRR12463381 GSM4729709 intestine nan Select Strain 20dph Biological Rep5 nan
          SRR12463382 GSM4729710 intestine nan Commercial Strain 65dph Biological Rep1 nan
          SRR12463383 GSM4729711 intestine nan Commercial Strain 65dph Biological Rep2 nan
          SRR12463384 GSM4729712 intestine nan Commercial Strain 65dph Biological Rep3 nan
          SRR12463385 GSM4729713 intestine nan Commercial Strain 65dph Biological Rep4 nan
          SRR12463386 GSM4729714 intestine nan Commercial Strain 65dph Biological Rep5 nan
          SRR12463387 GSM4729715 intestine nan Select Strain 65dph Biological Rep1 nan
          SRR12463388 GSM4729716 intestine nan Select Strain 65dph Biological Rep2 nan
          SRR12463389 GSM4729717 intestine nan Select Strain 65dph Biological Rep3 nan
          SRR12463390 GSM4729718 intestine nan Select Strain 65dph Biological Rep4 nan
          SRR12463391 GSM4729719 intestine nan Select Strain 65dph Biological Rep5 nan
    • PRJNA287641:
          transcriptome of rainbow trout with extremely high and low carcass fat content in a strain
      • key word
        • Baseline; BINDING-PROTEINS; GENE-EXPRESSION; 2-WAY SELECTION; RNA-SEQ; INSULIN; MUSCLE; LIPOGENESIS; ACTIVATION; TRAITS; TOPHAT
      • publication
        • Peng, et al. "Transcriptome Analyses Reveal Lipid Metabolic Process in Liver Related to the Difference of Carcass Fat Content in Rainbow Trout (Oncorhynchus mykiss).".
      • abstract
        • Excessive accumulation of carcass fat in farm animals, including fish, has a significant impact on meat quality and on the cost of feeding. Similar to farmed animals and humans, the liver can be considered one of the most important organs involved in lipid metabolism in rainbow trout (Oncorhynchus mykiss). RNA-seq based whole transcriptome sequencing was performed to liver tissue of rainbow trout with high and low carcass fat content in this study. In total 1,694 differentially expressed transcripts were identified, including many genes involved in lipid metabolism, such as L-FABP,adiponectin, PPAR-α, PPAR-β, and IGFBP1a. Evidence presented in this study indicated that lipid metabolic process in liver may be related to the difference of carcass fat content. The relevance of PPAR-α and PPAR-β as molecular markers for fat storage in liver should be worthy of further investigation.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR2072562 liver tissue in rainbow trout (Oncorhynchus mykiss) with extremely high and low carcass fat content liver nan Transcriptional profiling of liver tissue in rainbow trout (Oncorhynchus mykiss) with extremely high and low carcass fat content by RNA-sequencing nan
          SRR3184766 RTLF white muscle nan Transcriptional profiling of liver tissue in rainbow trout (Oncorhynchus mykiss) with extremely high and low carcass fat content by RNA-sequencing nan
    • PRJNA269115:
          RNA seq data from rainbow trout investigating the genetic basis of smoltification.
      • key word
        • Baseline; [1]Salmonidae; Ohnologs; Homeologs; Differential Gene Expression; Smoltification; ONCORHYNCHUS-TSHAWYTSCHA; GENE-EXPRESSION; EVOLUTION; POLYPLOIDY; REVEALS; RAINBOW; DOSAGE; PLANTS; TROUT; DIVERGENCE [2]MIGRATION-RELATED TRAITS; GROWTH-HORMONE; X-CHROMOSOME; Y-CHROMOSOME; DIMORPHISM; EVOLUTION; SELECTION; DIFFERENTIATION; SALMON; ARCHITECTURE
      • publication
        • [1]Campbell, M. A. , et al. "Long-Term Conservation of Ohnologs Through Partial Tetrasomy Following Whole-Genome Duplication in Salmonidae." G3-Genes Genomes Genetics 9.6(2019):g3.400070.2019. [2]Hale MC, et al. "Evidence of sex-bias in gene expression in the brain transcriptome of two populations of rainbow trout (Oncorhynchus mykiss) with divergent life histories", Plos One, 2018; 13:2
      • abstract
        • [1]Whole-genome duplications (WGDs) have occurred repeatedly and broadly throughout the evolutionary history of eukaryotes. However, the effects of WGD on genome function and evolution remain unclear. The salmonid WGD that occurred approximately 88 million years ago presents an excellent opportunity for studying the effects of WGD as similar to 10-15% of each salmonid genome still exhibits tetrasomic inheritance. Herein, we utilized the rainbow trout (Oncorhynchus mykiss) genome assembly and brain transcriptome data to examine the fate of gene pairs (ohnologs) following the salmonid whole-genome duplication. We find higher sequence identity between ohnologs located within known tetrasomic regions than between ohnologs found in disomic regions, and that tetrasomically inherited ohnologs showed greater similarity in patterns of gene expression and per ohnolog were lower expressed, than disomically inherited ohnologs. Enrichment testing for Gene Ontology terms identified 49 over-represented terms in tetrasomically inherited ohnologs compared to disomic ohnologs. However, why these ohnologs are retained as tetrasomic is difficult to answer. It could be that we have identified salmonid specific "dangerous duplicates", that is, genes that cannot take on new roles following WGD. Alternatively, there may be adaptive advantages for retaining genes as functional duplicates in tetrasomic regions, as presumably, movement of these genes into disomic regions would affect both their sequence identity and their gene expression patterns. [2]Sex-bias in gene expression is a mechanism that can generate phenotypic variance between the sexes, however, relatively little is known about how patterns of sex-bias vary during development, and how variable sex-bias is between different populations. To that end, we measured sex-bias in gene expression in the brain transcriptome of rainbow trout (Oncorhynchus mykiss) during the first two years of development. Our sampling included from the fry stage through to when O. mykiss either migrate to the ocean or remain resident and undergo sexual maturation. Samples came from two F-1 lines: One from migratory steel-head trout and one from resident rainbow trout. All samples were reared in a common garden environment and RNA sequencing (RNA-seq) was used to estimate patterns of gene expression. A total of 1,716 (4.6% of total) genes showed evidence of sex-bias in gene expression in at least one time point. The majority (96.7%) of sex-biased genes were differentially expressed during the second year of development, indicating that patterns of sex-bias in expression are tied to key developmental events, such as migration and sexual maturation. Mapping of differentially expressed genes to the O. mykiss genome revealed that the X chromosome is enriched for female upregulated genes, and this may indicate a lack of dosage compensation in rainbow trout. There were many more sex-biased genes in the migratory line than the resident line suggesting differences in patterns of gene expression in the brain between populations subjected to different forces of selection. Overall, our results suggest that there is considerable variation in the extent and identity of genes exhibiting sex-bias during the first two years of life. These differentially expressed genes may be connected to developmental differences between the sexes, and/or between adopting a resident or migratory life history.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR1798255 4079 Whole Brain not collected nan nan
          SRR1798265 4089 Whole Brain not collected nan nan
          SRR1798258 4082 Whole Brain not collected nan nan
          SRR1798256 4080 Whole Brain not collected nan nan
          SRR1798266 4090 Whole Brain not collected nan nan
          SRR1798275 4099 Whole Brain not collected nan nan
          SRR1798254 4078 Whole Brain not collected nan nan
          SRR1798257 4081 Whole Brain not collected nan nan
          SRR1798260 4084 Whole Brain not collected nan nan
          SRR1798261 4085 Whole Brain not collected nan nan
          SRR1798263 4087 Whole Brain not collected nan nan
          SRR1798271 4095 Whole Brain not collected nan nan
          SRR1798276 4100 Whole Brain not collected nan nan
          SRR1798267 4091 Whole Brain not collected nan nan
          SRR1798269 4093 Whole Brain not collected nan nan
          SRR1798270 4094 Whole Brain not collected nan nan
          SRR1798273 4097 Whole Brain not collected nan nan
          SRR1798274 4098 Whole Brain not collected nan nan
          SRR1798268 4092 Whole Brain not collected nan nan
          SRR1798262 4086 Whole Brain not collected nan nan
          SRR1798272 4096 Whole Brain not collected nan nan
          SRR1798264 4088 Whole Brain not collected nan nan
          SRR1798259 4083 Whole Brain not collected nan nan
    • PRJNA257002:
          Transcriptome analysis of the rainbow trout egg
      • key word
        • Baseline; Gene duplication; Teleosts; Holostean; Gene expression; Gar; Salmonids; Assembly;Stra8; Mcam; SPOTTED GAR; DIVERSIFICATION; RESOLUTION; PHYLOGENY; STRA8; CD146; TIME
      • publication
        • Pasquier J et al., "Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.", BMC Genomics, 2016 May 18;17:368
      • abstract
        • With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several wholegenome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fishin human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finnedfish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study theevolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR1533639 D2_Om_14 Unfertilized eggs nan Autumn-spawning. Rainbow trout unfertilized eggs nan
    • PRJNA644781:
          Comparative transcriptome analysis of the skin reveals the innate immunity difference between wild-type and yellow mutant rainbow trout (rainbow trout)
      • key word
        • Baseline, skin, mutant, immunity
      • publication
        • nan
      • abstract
        • Purpose: The goal of this study is to identify the difference of immunity between wild-type and yellow mutant rainbow trout in natural flowing water pond culture environment. Methods: The transcriptomic profiles of the skin were generated by using the Hiseq™4000 sequencing platform. Results: A total of 557,976,332 clean reads were yielded from six libraries and then assembled into 38,226 genes. Using P-value of 0.05 as the threshold, 3373 differentially expressed genes (DEGs) were obtained between WR_S and YR_S rainbow trout skin including the members of HSP90, V-ATPases, GST, SUGT1, NLRP3, NOD1, TLR3, IFR3, DHX58, IFIH1, JAK1, JAK2, STAT1 and NAMPT (|log2 fold-change| ranged from 1 to 4). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were performed. A majority of DEGs were enriched in innate immune-related GO terms and pathways, such as activation of innate immune response, inflammatory response, innate immune response, NAD+ADP-ribosyltransferase activity and NAD biosynthetic process in sub-categories of GO terms, and RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, Phagosome, Jak-STAT signaling pathway in KEGG enrichment pathways. Meanwhile, several immune-related metabolic pathways were also identified including metabolism of Xenobiotics by cytochrome P450, Glutathione metabolism, Nicotinate and nicotinamide metabolism. Additionally, 15 DEGs were selected and validated their expression level by qRT-PCR to confirm accuracy of the RNA-seq. Conclusions: Our study is the first time to clarify the skin innate immunity difference between wild-type and yellow mutant rainbow trout in the natural flowing water pond culture environment. Our results show that the expression of most immune-related genes in the corresponding pathways were up-regulated in WR_S rainbow trout. We presumed that the disease resistance of WR_S rainbow trout might be stronger than YR_S rainbow trout. Overall design: The transcriptomic profiles of the skin from wild-type and yellow mutant cultured in the natural flowing water pond culture environment were generated by using the Hiseq™4000 sequencing platform
      • sample list
        • sample id sample name tissue strain treatment description
          SRR12171314 GSM4661599 dorsal skin nan wild-type nan
          SRR12171315 GSM4661600 dorsal skin nan wild-type nan
          SRR12171316 GSM4661601 dorsal skin nan wild-type nan
          SRR12171317 GSM4661602 dorsal skin nan yellow mutant nan
          SRR12171318 GSM4661603 dorsal skin nan yellow mutant nan
          SRR12171319 GSM4661604 dorsal skin nan yellow mutant nan
  • challenge
    • PRJNA659524:
          Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during baterial infection with Flavobacterium psychrophilum (rainbow trout)
      • key word
        • Challenge, strain, high growth rates, immune performance, Flavobacterium psychrophilum
      • publication
        • nan
      • abstract
        • Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain also shows superior performance in bacterial and viral disease challenges compared to commercial trout strains, and even a strain specifically selected over many generations for viral and bacterial disease resistance. The selection criteria was strictly focused on performance on plant-based diets, and therefore the physiological mechanisms responsible for the strain’s superior disease resistance remain unresolved. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the intestinal gene expression of the select strain to that of a commercial control line of trout during an experimental bacterial infection with Flavobacterium psychrophilum (Fp) (CSF 259-93), the causative agent of bacterial cold water disease (BCWD) in salmonids. At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. For both strains of trout, three tanks of fish were experimentally infected with Fp by intramuscular injection and one control tank was mock challenged by sham injection. Sampling was conducted at 5 days post challenge (dpc) (Early Infection) and 21 dpc (Late/Recovered Infection). Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. The select strain of trout showed significantly better survival rates (Log-Rank Test, p < 0.0001) over the 21 day infection period, with 70 and 95 % mortality among the select and commercial strain, respectively. Reads from the RNAseq samples were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the strains of trout, infection time points, and disease status. Overall design: At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. There were three infected tanks and one mock challenged tank per strain. Intestinal samples were collected from all tanks at 5 days post challenge (dpc) and 21 dpc. Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. At each time point, there are 6 pooled samples of infected fish and 2 pooled samples of mock challenged fish per strain. However, due to high mortality in the commercial strain, only one tank of infected commercial trout was sampled at 21 dpc.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR12523305 GSM4748358 intestine Flavobacterium psychrophilum TF1-21dpc-1: Commercial 21dpc BCWD TF1 BiologicalRep1 nan
          SRR12523306 GSM4748359 intestine Flavobacterium psychrophilum TF1-21dpc-2: Commercial 21dpc BCWD TF1 BiologicalRep2 nan
          SRR12523307 GSM4748360 intestine Flavobacterium psychrophilum TFC-21dpc-1: Commercial 21dpc BCWD_Sham TFControl BiologicalRep1 nan
          SRR12523308 GSM4748361 intestine Flavobacterium psychrophilum TFC-21dpc-2: Commercial 21dpc BCWD_Sham TFControl BiologicalRep2 nan
          SRR12523309 GSM4748362 intestine Flavobacterium psychrophilum CF1-21dpc-1: Select 21dpc BCWD CF1 BiologicalRep1 nan
          SRR12523310 GSM4748363 intestine Flavobacterium psychrophilum CF1-21dpc-2: Select 21dpc BCWD CF1 BiologicalRep2 nan
          SRR12523311 GSM4748364 intestine Flavobacterium psychrophilum CF2-21dpc-1: Select 21dpc BCWD CF2 BiologicalRep1 nan
          SRR12523312 GSM4748365 intestine Flavobacterium psychrophilum CF2-21dpc-2: Select 21dpc BCWD CF2 BiologicalRep2 nan
          SRR12523313 GSM4748366 intestine Flavobacterium psychrophilum CF3-21dpc-1: Select 21dpc BCWD CF3 BiologicalRep1 nan
          SRR12523314 GSM4748367 intestine Flavobacterium psychrophilum CF3-21dpc-2: Select 21dpc BCWD CF3 BiologicalRep2 nan
          SRR12523315 GSM4748368 intestine Flavobacterium psychrophilum CFC-21dpc-1: Select 21dpc BCWD_Sham CFControl BiologicalRep1 nan
          SRR12523316 GSM4748369 intestine Flavobacterium psychrophilum CFC-21dpc-2: Select 21dpc BCWD_Sham CFControl BiologicalRep2 nan
          SRR12523317 GSM4748370 intestine Flavobacterium psychrophilum TF1-5dpc-1: Commercial 5dpc BCWD TF1 BiologicalRep1 nan
          SRR12523318 GSM4748371 intestine Flavobacterium psychrophilum TF1-5dpc-2: Commercial 5dpc BCWD TF1 BiologicalRep2 nan
          SRR12523319 GSM4748372 intestine Flavobacterium psychrophilum TF2-5dpc-1: Commercial 5dpc BCWD TF2 BiologicalRep1 nan
          SRR12523320 GSM4748373 intestine Flavobacterium psychrophilum TF2-5dpc-2: Commercial 5dpc BCWD TF2 BiologicalRep2 nan
          SRR12523321 GSM4748374 intestine Flavobacterium psychrophilum TF3-5dpc-1: Commercial 5dpc BCWD TF3 BiologicalRep1 nan
          SRR12523322 GSM4748375 intestine Flavobacterium psychrophilum TF3-5dpc-2: Commercial 5dpc BCWD TF3 BiologicalRep2 nan
          SRR12523323 GSM4748376 intestine Flavobacterium psychrophilum TFC-5dpc-1: Commercial 5dpc BCWD_Sham TFControl BiologicalRep1 nan
          SRR12523324 GSM4748377 intestine Flavobacterium psychrophilum TFC-5dpc-2: Commercial 5dpc BCWD_Sham TFControl BiologicalRep2 nan
          SRR12523325 GSM4748378 intestine Flavobacterium psychrophilum CF1-5dpc-1: Select 5dpc BCWD CF1 BiologicalRep1 nan
          SRR12523326 GSM4748379 intestine Flavobacterium psychrophilum CF1-5dpc-2: Select 5dpc BCWD CF1 BiologicalRep2 nan
          SRR12523327 GSM4748380 intestine Flavobacterium psychrophilum CF2-5dpc-1: Select 5dpc BCWD CF2 BiologicalRep1 nan
          SRR12523328 GSM4748381 intestine Flavobacterium psychrophilum CF2-5dpc-2: Select 5dpc BCWD CF2 BiologicalRep2 nan
          SRR12523329 GSM4748382 intestine Flavobacterium psychrophilum CF3-5dpc-1: Select 5dpc BCWD CF3 BiologicalRep1 nan
          SRR12523330 GSM4748383 intestine Flavobacterium psychrophilum CF3-5dpc-2: Select 5dpc BCWD CF3 BiologicalRep2 nan
          SRR12523331 GSM4748384 intestine Flavobacterium psychrophilum CFC-5dpc-1: Select 5dpc BCWD_Sham CFControl BiologicalRep1 nan
          SRR12523332 GSM4748385 intestine Flavobacterium psychrophilum CFC-5dpc-2: Select 5dpc BCWD_Sham CFControl BiologicalRep2 nan
    • PRJNA658476:
          Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during infection with infectious hematopoietic necrosis virus (rainbow trout)
      • key word
        • Challenge, strain, high growth rates, immune performance, hematopoietic necrosis virus
      • publication
        • nan
      • abstract
        • Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain also shows superior performance in bacterial and viral disease challenges compared to commercial trout strains, and even a strain specifically selected over many generations for viral and bacterial disease resistance. The selection criteria was strictly focused on performance on plant-based diets, and therefore the physiological mechanisms responsible for the strain’s superior disease resistance remain unresolved. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the intestinal gene expression of the select strain to that of a commercial control line of trout during an experimental viral infection using the CSF 220-90 isolate of Infectious Hematopoietic Necrosis virus (IHNv). At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. For both strains of trout, three tanks of fish were experimentally infected with IHNv by static bath and one tank was mock challenged by static bath (Sham). Sampling was conducted at 4 days post challenge (dpc) (Early Infection) and 20 dpc (Late/Recovered Infection). Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. Infections were mild with mortality rates near 50% over the 21 day trial and no significant difference in mortality rates between the two strains of trout. Reads from the RNAseq samples were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the strains of trout, infection time points, and disease status. Overall design: At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. There were three infected tanks and one mock challenged tank per strain. Intestinal samples were collected from all groups at 4 days post challenge (dpc) and 20 dpc. Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. At each time point, there are 6 pooled samples of infected fish and 2 pooled samples of mock challenged fish per strain.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR12491281 GSM4734541 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI1 BiologicalRep1 nan
          SRR12491282 GSM4734542 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI1 BiologicalRep2 nan
          SRR12491283 GSM4734543 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI2 BiologicalRep1 nan
          SRR12491284 GSM4734544 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI2 BiologicalRep2 nan
          SRR12491285 GSM4734545 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI3 BiologicalRep1 nan
          SRR12491286 GSM4734546 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI3 BiologicalRep2 nan
          SRR12491287 GSM4734547 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV_Sham TIControl BiologicalRep1 nan
          SRR12491288 GSM4734548 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV_Sham TIControl BiologicalRep2 nan
          SRR12491289 GSM4734549 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI1 BiologicalRep1 nan
          SRR12491290 GSM4734550 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI1 BiologicalRep2 nan
          SRR12491291 GSM4734551 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI2 BiologicalRep1 nan
          SRR12491292 GSM4734552 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI2 BiologicalRep2 nan
          SRR12491293 GSM4734553 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI3 BiologicalRep1 nan
          SRR12491294 GSM4734554 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI3 BiologicalRep2 nan
          SRR12491295 GSM4734555 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV_Sham CIControl BiologicalRep1 nan
          SRR12491296 GSM4734556 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV_Sham CIControl BiologicalRep2 nan
          SRR12491297 GSM4734557 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI1 BiologicalRep1 nan
          SRR12491298 GSM4734558 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI1 BiologicalRep2 nan
          SRR12491299 GSM4734559 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI2 BiologicalRep1 nan
          SRR12491300 GSM4734560 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI2 BiologicalRep2 nan
          SRR12491301 GSM4734561 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI3 BiologicalRep1 nan
          SRR12491302 GSM4734562 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI3 BiologicalRep2 nan
          SRR12491303 GSM4734563 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV_Sham TIControl BiologicalRep1 nan
          SRR12491304 GSM4734564 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV_Sham TIControl BiologicalRep2 nan
          SRR12491305 GSM4734565 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI1 BiologicalRep1 nan
          SRR12491306 GSM4734566 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI1 BiologicalRep2 nan
          SRR12491307 GSM4734567 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI2 BiologicalRep1 nan
          SRR12491308 GSM4734568 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI2 BiologicalRep2 nan
          SRR12491309 GSM4734569 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI3 BiologicalRep1 nan
          SRR12491310 GSM4734570 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI3 BiologicalRep2 nan
          SRR12491311 GSM4734571 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV_Sham CIControl BiologicalRep1 nan
          SRR12491312 GSM4734572 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV_Sham CIControl BiologicalRep2 nan
    • PRJNA295899:
          Whole transcriptome of fishes injected with inactivated Yersinia ruckeri cells or PBS.
      • key word
        • Challenge, Yersinia ruckeri cells, PBS
      • publication
        • Michela, F. , et al. "Induced expression of cathelicidins in trout (Oncorhynchus mykiss) challenged with four different bacterial pathogens." Journal of Peptide ence 24(2018):e3089.
      • abstract
        • Cathelicidins are an important family of antimicrobial peptide effectors of innate immunity in vertebrates. Two members of this group, CATH‐1 and CATH‐2, have been identified and characterized in teleosts (ray‐finned fish). In this study, we investigated the expression of these genes in different tissues of rainbow trout challenged with 4 different inactivated pathogens. By using qPCR, we detected a strong induction of bothcath‐1 and cath‐2 genes within 24 hours after intraperitoneal inoculation withLactococcus garvieae, Yersinia ruckeri, Aeromonas salmonicida, or Flavobacterium psychrophilum cells. Up to 700‐fold induction of cath‐2 was observed in the spleen of animals challenged with Y. ruckeri. Moreover, we found differences in the intensity and timing of gene up‐regulation in the analyzed tissues. The overall results highlight the importance of cathelicidins in the immune response mechanisms of salmonids.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR2598319 TR_kidney kidney Yersinia ruckeri animal sample from Oncorhynchus mykiss nan
          SRR2598320 TR_kidney kidney Yersinia ruckeri animal sample from Oncorhynchus mykiss nan
          SRR2598327 TR_spleen spleen Yersinia ruckeri animal sample from Oncorhynchus mykiss nan
          SRR2598325 TR_spleen spleen Yersinia ruckeri animal sample from Oncorhynchus mykiss nan
          SRR2598324 TR_spleen spleen Yersinia ruckeri animal sample from Oncorhynchus mykiss nan
          SRR2598328 TR_spleen spleen Yersinia ruckeri animal sample from Oncorhynchus mykiss nan
    • PRJNA271198:
          To obtain differentially expressed genes and their functions by comparasion and statistical analysis
      • key word
        • Challenge; Rainbow trout; A. salmonicida; Furunculosis; Spleen; Transcriptome; Proteome; DIFFERENTIALLY EXPRESSED GENES; DC-SIGN; QUANTITATIVE PROTEOMICS; RESPONSIVE PROTEINS; ANTIBODY-RESPONSE; SALMO-GAIRDNERI; IDENTIFICATION; MACROPHAGES; CHANNEL; GILL
      • publication
        • Long, et al. "Transcriptomic and proteomic analyses of splenic immune mechanisms of rainbow trout (Oncorhynchus mykiss) infected by Aeromonas salmonicida subsp salmonicida." Journal of proteomics 122(2015):41-54.
      • abstract
        • Furunculosis caused by Aeromonas salmonicida subsp. salmonicida is an epidemic disease among salmonids, including rainbow trout (Oncorhynchus mykiss). However, the immune mechanisms that are elicited in rainbow trout against the invasion ofA. salmonicida are not yet fully understood. In this study, we examined the spleen to investigate the immune response of rainbow trout at 3 days post-infection by A. salmonicida at the transcriptome and proteome levels by using Illumina-seq and iTRAQ methods, respectively. A total of 1036 genes and 133 proteins were found to undergo differential expression during the immune response of the spleen againstA. salmonicida infection. Gene ontology and KEGG analysis were conducted among the differentially expressed genes and proteins, revealing that immune system process and response to stimulus were the top two biological processes, and immune system, signaling molecules and interaction, and immune diseases were the differential pathways activated. Correlation analysis of transcriptomic andproteomic results showed 17 proteins (11 upregulated and 6 downregulated) having consistent expression at RNA and protein levels. Moreover, protein–protein interaction analysis showed that diseases, proteasome, aminoacyl-tRNAbiosynthesis, and nucleotide metabolism were the main interactions among the consistently expressed proteins. Consequently, these upregulated proteins, namely,ferritin, CD209, IL13Rα1, VDAC2, GIMAP7, PSMA1, and two ANXA11s could be considered as potential biomarkers for rainbow trout immune responses.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR1735393 IS spleen Aeromonas salmonicida Spleen sample from infected Rainbow trout nan
          SRR1735395 HS spleen Aeromonas salmonicida Spleen sample from healthy Rainbow trout nan
  • chemical
    • PRJNA397221:
          Oncorhynchus mykiss trasncriptomic response to benzotriazole UV stabilizers
      • key word
        • Chemical; Emerging contaminants; Mixture toxicology; Freshwater fish; Ecotoxicogenomics; Iron homeostasis; In vivo exposure; SUBSTITUTED DIPHENYLAMINE ANTIOXIDANTS; UV STABILIZERS; MASS-SPECTROMETRY; URBAN CREEK; EXPRESSION; GENES; BIOACCUMULATION; ABSORBENTS; EXTRACTION; ESTUARINE
      • publication
        • Giraudo, M. , et al. "Food‐Borne Exposure of Juvenile Rainbow Trout (Oncorhynchus mykiss) to Benzotriazole Ultraviolet Stabilizers Alone and in Mixture Induces Specific Transcriptional Changes", Environmental Toxicology and Chemistry 39.4(2020).
      • abstract
        • Benzotriazole ultraviolet‐stabilizers (BZT‐UVs) are commonly used as additives to protect from light‐induced degradation in a variety of consumer goods. Despite their widespread presence in aquatic ecosystems, information on the effects of these compounds remains largely unknown. The objectives of the present study were to evaluate the chronic effects of 2 BZT‐UVs alone and in a mixture, 2‐(2H‐benzotriazol‐2‐yl)‐4,6‐bis(1‐methyl‐1‐phenylethyl)phenol (UV‐234) and 2‐(2H‐benzotriazol‐2‐yl)‐4,6‐di‐tert‐pentylphenol (UV‐328), in juvenile rainbow trout (Oncorhynchus mykiss) chronically exposed (for 28 d) through the diet. Chemical analyses of livers from exposed trout suggested liver accumulation and potential metabolism of the 2 compounds. Hepatic RNA‐sequencing analyses revealed specific effects of each compound on gene transcription profiles; UV‐234 affected mainly genes involved in cellular metabolism, whereas UV‐328 induced the transcription of ribosomal proteins and downregulated genes involved in immune responses. Both compounds regulated iron homeostasis genes in an opposite manner. The mixture of both BZT‐UVs did not produce significant evidence of additive or synergistic effects. Environ Toxicol Chem 2020;39:852–862. © 2020 Her Majesty the Queen in Right of Canada.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR5950209 CA-234-7 liver nan UV-234 nan
          SRR5950211 T-234-2 liver nan UV-234 nan
          SRR5950212 T-234-1 liver nan UV-234 nan
          SRR5950213 CA-234-3 liver nan UV-234 nan
          SRR5950214 CA-234-1 liver not applicable UV-234 nan
          SRR5950215 CA-234-5 liver nan UV-234 nan
          SRR5950222 T-MIX-1 liver nan UV-234+UV-328 nan
          SRR5950223 T-MIX-4 liver nan UV-234+UV-328 nan
          SRR5950224 T-MIX-3 liver nan UV-234+UV-328 nan
          SRR5950225 CA-328-7 liver nan UV-328 nan
          SRR5950228 CA-328-4 liver nan UV-328 nan
          SRR5950229 CA-328-2 liver nan UV-328 nan
          SRR5950230 CA-328-1 liver nan UV-328 nan
          SRR5950233 T-329-3 liver nan UV-328 nan
          SRR5950236 CA-MIX-6 liver nan UV-234+UV-328 nan
          SRR5950239 CA-MIX-1 liver nan UV-234+UV-328 nan
          SRR5950240 CA-MIX-2 liver nan UV-234+UV-328 nan
          SRR5950242 T-328-7 liver nan UV-328 nan
          SRR5950243 T-328-4 liver nan UV-328 nan
          SRR5950219 T-MIX-6 liver nan UV-234+UV-328 nan
          SRR5950220 T-MIX-5 liver nan UV-234+UV-328 nan
          SRR5950232 T-234-5 liver nan UV-234 nan
          SRR5950235 CA-MIX-5 liver nan UV-234+UV-328 nan
          SRR5950226 CA-328-6 liver nan UV-328 nan
          SRR5950217 T-234-4 liver nan UV-234 nan
          SRR5950216 CA-234-4 liver nan UV-234 nan
          SRR5950221 T-MIX-2 liver nan UV-234+UV-328 nan
          SRR5950238 CA-MIX-4 liver nan UV-234+UV-328 nan
          SRR5950227 CA-328-5 liver nan UV-328 nan
          SRR5950234 T-328-1 liver nan UV-328 nan
          SRR5950244 T-328-5 liver nan UV-328 nan
          SRR5950231 T-234-6 liver nan UV-234 nan
          SRR5950237 CA-MIX-3 liver nan UV-234+UV-328 nan
          SRR5950241 T-328-6 liver nan UV-328 nan
          SRR5950210 CA-234-6 liver nan UV-234 nan
          SRR5950218 T-234-3 liver nan UV-234 nan
    • PRJNA369238:
          Multigenerational shifts in liver molecular programming in rainbow trout raised from bisphenol A-laden eggs
      • key word
        • Chemical; DNA METHYLATION; BPA EXPOSURE; LIFE STAGES; FISH; CHOLESTEROL; ATLANTIC; METABOLISM; DISRUPTS; IMPACTS; MEDAKA
      • publication
        • Sadoul B et al., "Bisphenol A in eggs causes development-specific liver molecular reprogramming in two generations of rainbow trout.", Sci Rep, 2017 Oct 26;7(1):14131
      • abstract
        • Bisphenol A (BPA) is widely used in the manufacture of plastics and epoxy resins and is prevalent in the aquatic environment. BPA disrupts endocrine pathways in fish, but the long-term developmental implications are unknown. We demonstrate that BPA deposition in the eggs of rainbow trout(Oncorhynchus mykiss), an ecologically and economically important species of fish, reprograms liver metabolism in the offspring and alters the developmental growth trajectory in two generations. Specifically, BPA reduces growth during early development, followed by a catch-up growth post-juveniles. More importantly, we observed a developmental shift in the liver transcriptome, including an increased propensity for protein breakdown during early life stages to lipid and cholesterol synthesis post-juveniles. The liver molecular responses corresponded with the transient growth phenotypes observed in the F1 generation, and this was also evident in the F2 generation. Altogether, maternal and/or ancestral embryonic exposure to BPA affects livermetabolism leading to development-distinct effects on growth, underscoring the need for novel risk assessment strategies for this chemical in the aquatic environment. This is particularly applicable to migratory species, such as salmon, where distinct temporal changes in growth and physiology during development are critical for their spawning success.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR5217794 GSM2472231 liver nan Control nan
          SRR5217822 GSM2472259 liver nan 4 ng BPA nan
          SRR5217831 GSM2472268 liver nan Control nan
          SRR5217837 GSM2472274 liver nan 4 ng BPA nan
          SRR5217800 GSM2472237 liver nan 4 ng BPA nan
          SRR5217811 GSM2472248 liver nan 4 ng BPA nan
          SRR5217827 GSM2472264 liver nan 40 ng BPA nan
          SRR5217795 GSM2472232 liver nan Control nan
          SRR5217797 GSM2472234 liver nan Control nan
          SRR5217799 GSM2472236 liver nan 4 ng BPA nan
          SRR5217801 GSM2472238 liver nan 4 ng BPA nan
          SRR5217802 GSM2472239 liver nan 40 ng BPA nan
          SRR5217803 GSM2472240 liver nan 40 ng BPA nan
          SRR5217804 GSM2472241 liver nan 40 ng BPA nan
          SRR5217805 GSM2472242 liver nan 40 ng BPA nan
          SRR5217806 GSM2472243 liver nan Control nan
          SRR5217807 GSM2472244 liver nan Control nan
          SRR5217810 GSM2472247 liver nan 4 ng BPA nan
          SRR5217813 GSM2472250 liver nan 4 ng BPA nan
          SRR5217814 GSM2472251 liver nan 40 ng BPA nan
          SRR5217815 GSM2472252 liver nan 40 ng BPA nan
          SRR5217816 GSM2472253 liver nan 40 ng BPA nan
          SRR5217819 GSM2472256 liver nan Control nan
          SRR5217821 GSM2472258 liver nan Control nan
          SRR5217823 GSM2472260 liver nan 4 ng BPA nan
          SRR5217824 GSM2472261 liver nan 4 ng BPA nan
          SRR5217825 GSM2472262 liver nan 4 ng BPA nan
          SRR5217828 GSM2472265 liver nan 40 ng BPA nan
          SRR5217830 GSM2472267 liver nan Control nan
          SRR5217833 GSM2472270 liver nan Control nan
          SRR5217834 GSM2472271 liver nan 4 ng BPA nan
          SRR5217835 GSM2472272 liver nan 4 ng BPA nan
          SRR5217826 GSM2472263 liver nan 40 ng BPA nan
          SRR5217796 GSM2472233 liver nan Control nan
          SRR5217818 GSM2472255 liver nan Control nan
          SRR5217829 GSM2472266 liver nan 40 ng BPA nan
          SRR5217836 GSM2472273 liver nan 4 ng BPA nan
          SRR5217839 GSM2472276 liver nan 40 ng BPA nan
          SRR5217832 GSM2472269 liver nan Control nan
          SRR5217820 GSM2472257 liver nan Control nan
          SRR5217809 GSM2472246 liver nan Control nan
          SRR5217812 GSM2472249 liver nan 4 ng BPA nan
          SRR5217817 GSM2472254 liver nan 40 ng BPA nan
          SRR5217798 GSM2472235 liver nan 4 ng BPA nan
          SRR5217838 GSM2472275 liver nan 40 ng BPA nan
          SRR5217840 GSM2472277 liver nan 40 ng BPA nan
          SRR5217808 GSM2472245 liver nan Control nan
          SRR5217841 GSM2472278 liver nan 40 ng BPA nan
    • PRJNA336343:
          Oncorhynchus mykiss transcriptomic response to brominated flame retardants
      • key word
        • Chemical, RNA-sequencing, Rainbow trout, Flame retardants, BTBPE, EHTBB, Gene transcription; ST-LAWRENCE-RIVER; ENDOCRINE-DISRUPTING CHEMICALS; GREAT-LAKES ATMOSPHERE; PERCH PERCA-FLAVESCENS; HERRING GULL EGGS; IN-VITRO; OREOCHROMIS-NILOTICUS; FIREMASTER(R) BZ-54; MESSENGER-RNA; NILE TILAPIA
      • publication
        • Giraudo, M. , et al. "Effects of food-borne exposure of juvenile rainbow trout (Oncorhynchus mykiss) to emerging brominated flame retardants 1,2-bis(2,4,6-tribromophenoxy)ethane and 2-ethylhexyl-2,3,4,5-tetrabromobenzoate." Aquatic Toxicology 186(2017):40-49.
      • abstract
        • Brominated flame retardants (BFRs) represent a large group of chemicals used in a variety of household and commercial products to prevent fire propagation. The environmental persistence and toxicity of some of the most widely used BFRs has resulted in a progressive ban worldwide and the development of novel BFRs for which the knowledge on environmental health impacts remains limited. The objectives of this study were to evaluate the effects of two emerging BFRs, 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE) and 2-ethylhexyl-2,3,4,5-tetrabromobenzoate (EH-TBB), in diet exposed juvenile rainbow trout (Oncorhynchus mykiss). Both compounds were detected in fish carcasses at 76% and 2% of the daily dosage of BTBPE and EH-TBB, respectively, indicating accumulation of BTBPE and by contrast extensive depuration/metabolism of EH-TBB. Liver gene transcription analysis using RNA-sequencing indicated that the chronic 28-d dietary exposure of trout to EH-TBB down-regulated one single gene related to endocrine-mediated processes, whereas BTBPE impacted the transcription of 33 genes, including genes involved in the immune response, reproduction, and oxidative stress. Additional analysis using qRT-PCR after 48-h and 28-d of exposure confirmed the impact of BTBPE on immune related genes in the liver (apolipoprotein A-I, lysozyme) and the head-kidney (complement c3-4). However, the activity of lysozymes measured at the protein level did not reflect transcriptomic results. Overall, results suggested an impact on immune-related gene transcription in BTBPE exposed fish, as well as oxidative stress and endocrine disruption potentials.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR4000188 EHTBB-C2 liver not applicable EHTBB nan
          SRR4000181 BTBPE-C3 liver not applicable BTBPE nan
          SRR4000185 BTBPE-3 liver not applicable BTBPE nan
          SRR4000173 BTBPE-C1 liver not applicable BTBPE nan
          SRR4000174 BTBPE-C2 liver not applicable BTBPE nan
          SRR4000176 EHTBB-C4 liver not applicable EHTBB nan
          SRR4000179 EHTBB-3 liver not applicable EHTBB nan
          SRR4000180 EHTBB-4 liver not applicable EHTBB nan
          SRR4000183 BTBPE-1 liver not applicable BTBPE nan
          SRR4000184 BTBPE-2 liver not applicable BTBPE nan
          SRR4000182 BTBPE-C4 liver not applicable BTBPE nan
          SRR4000175 EHTBB-C3 liver not applicable EHTBB nan
          SRR4000177 EHTBB-1 liver not applicable EHTBB nan
          SRR4000186 BTBPE-4 liver not applicable BTBPE nan
          SRR4000187 EHTBB-C1 liver not applicable EHTBB nan
          SRR4000178 EHTBB-2 liver not applicable EHTBB nan
    • PRJNA248395:
          The study undertook the sequencing of vertebrae from P-deficient and P-sufficient to understand the regulation of the vertebral bone.
      • key word
        • Chemical, P-sufficient, P-sufficient, vertebral bone
      • publication
        • nan
      • abstract
        • Phosphorus (P) deficiency triggers undermineralization of bone and vertebral deformities. To better understand the regulation of the vertebral bone, we undertook the sequencing of vertebrae from P-sufficient and P-sufficient. These data provide a reference for further quantitative studies on the role of P in the vertebral bone regulation.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR1508752 Troutvertebrae3 Vertebrae nan phosphorus-sufficient nan
          SRR1508754 Troutvertebrae2 Vertebrae nan phosphorus-deficient nan
          SRR1508757 Troutvertebrae5 Vertebrae nan phosphorus-deficient nan
          SRR1508759 Troutvertebrae4 Vertebrae nan phosphorus-deficient nan
          SRR1296551 Troutvertebrae1 Vertebrae nan nan nan
  • magnetic pulse
    • PRJNA391176:
          Effect of a pulsed magnetic field on gene expression in the retina of rainbow trout
      • key word
        • magnetic pulse, magnetite, magnetoreceptor, Oncorhynchus mykiss, eye, RNA-seq
      • publication
        • Robert RF et al. "Near absence of differential gene expression in the retina of rainbow trout after exposure to a magnetic pulse: implications for magnetoreception", Biology Letters, 2018; 14(6)20180209
      • abstract
        • The ability to perceive the Earth's magnetic field, or magnetoreception, exists in numerous animals. Although the mechanism underlying magnetoreception has not been clearly established in any species, in salmonid fish, it is hypothesized to occur by means of crystals of magnetite associated with nervous tissue such as the brain, olfactory organ or retina. In this study, rainbow trout (Oncorhynchus mykiss) were exposed to a brief magnetic pulse known to disrupt magnetic orientation behaviour in several animals. Changes in gene expression induced by the pulse were then examined in the retina. Analyses indicated that the pulse elicited differential expression of only a single gene,gamma-crystallin M3-like (crygm3). The near absence of an effect of the magnetic pulse on gene expression in the retina stands in sharp contrast to a recent study in which 181 genes were differentially expressed in brain tissue of O. mykiss after exposure to the same pulse. Overall, our results suggest either that magnetite-based magnetoreceptors in trout are not located in the retina, or else that they are unaffected by magnetic pulses that can disrupt magnetic orientation behaviour in animals.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR5738265 OJ0128L left_retina not applicable Pulsed nan
          SRR5738247 DS0138L left_retina not applicable Control nan
          SRR5738266 QI0167R right_retina not applicable Control nan
          SRR5738269 QM0198L left_retina not applicable Control nan
          SRR5738246 DS0138R right_retina not applicable Control nan
          SRR5738250 FI0058R right_retina not applicable Control nan
          SRR5738264 OJ0128R right_retina not applicable Pulsed nan
          SRR5738267 QI0167L left_retina not applicable Control nan
          SRR5738259 ZT0176R right_retina not applicable Pulsed nan
          SRR5738251 FI0058L left_retina not applicable Control nan
          SRR5738260 HZ0207R right_retina not applicable Pulsed nan
          SRR5738262 JQ0063R right_retina not applicable Pulsed nan
          SRR5738248 DC0053R right_retina not applicable Pulsed nan
          SRR5738263 JQ0063L left_retina not applicable Pulsed nan
          SRR5738252 DX0088R right_retina not applicable Pulsed nan
          SRR5738254 HN0056R right_retina not applicable Control nan
          SRR5738268 QM0198R right_retina not applicable Control nan
          SRR5738261 HZ0207L left_retina not applicable Pulsed nan
          SRR5738253 DX0088L left_retina not applicable Pulsed nan
          SRR5738258 ZT0176L left_retina not applicable Pulsed nan
          SRR5738256 XL0070L left_retina not applicable Control nan
          SRR5738255 HN0056L left_retina not applicable Control nan
          SRR5738257 XL0070R right_retina not applicable Control nan
          SRR5738249 DC0053L left_retina not applicable Pulsed nan
  • migration
    • PRJNA268960:
          RNAseq used to examine gene expression in divergent migrant and resident populations of rainbow trout that share a recent coancestry
      • key word
        • Migration; RNAseq; transcriptome; PARR-SMOLT TRANSFORMATION; RNA-SEQ DATA; ATLANTIC SALMON; CANDIDATE GENES; CHINOOK SALMON; GROWTH-HORMONE; RAINBOW-TROUT; THYROID-HORMONES; PACIFIC SALMON; COHO SALMON
      • publication
        • Mckinney, G. J. , et al. "Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss." Molecular Ecology 24.8(2015).
      • abstract
        • Little information has been gathered regarding the ontogenetic changes that contribute to differentiation between resident and migrant individuals, particularly before the onset of gross morphological and physiological changes in migratory individuals. The aim of this study was to evaluate gene expression during early development in Oncorhynchus mykiss populations with different life histories, in a tissue known to integrate environmental cues to regulate complex developmental processes and behaviours. We sampled offspring produced from migrant and resident parents, collecting whole embryos prior to the beginning of first feeding, and brain tissue at three additional time points over the first year of development. RNA sequencing for 32 individuals generated a reference transcriptome of 30177 genes that passed count thresholds. Differential gene expression between migrant and resident offspring was observed for 1982 genes. The greatest number of differentially expressed genes occurred at 8months of age, in the spring a full year before the obvious physiological transformation from stream-dwelling parr to sea water-adaptable smolts begins for migrant individuals. Sex and age exhibited considerable effects on differential gene expression between migrants and resident offspring. Differential gene expression was observed in genes previously associated with migration, but also in genes previously unassociated with early life history divergence. Pathway analysis revealed coordinated differential expression in genes related to phototransduction, which could modulate photoperiod responsiveness and variation in circadian rhythms. The role for early differentiation in light sensitivity and biological rhythms is particularly intriguing in understanding early brain processes involved in differentiation of migratory and resident life history types.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR1692327 Hatch_116-3 Embryo nan Sashin Lake nan
          SRR1692348 June_29-3 Brain nan Sashin Lake nan
          SRR1692351 Oct_3-1 Brain nan Sashin Creek nan
          SRR1692345 June_20-1 Brain nan Sashin Lake nan
          SRR1692300 Feb_2-3 Brain nan Sashin Creek nan
          SRR1692343 June_3-1 Brain nan Sashin Creek nan
          SRR1692311 Hatch_69-9 Embryo nan Sashin Creek nan
          SRR1692341 June_1-1 Brain nan Sashin Creek nan
          SRR1692344 June_6-1 Brain nan Sashin Creek nan
          SRR1692346 June_21-3 Brain nan Sashin Lake nan
          SRR1692302 Feb_3-5 Brain nan Sashin Creek nan
          SRR1692304 Feb_21-4 Brain nan Sashin Lake nan
          SRR1692308 Feb_29-5 Brain nan Sashin Lake nan
          SRR1692355 Oct_28-3 Brain nan Sashin Lake nan
          SRR1692299 Feb_1-2 Brain nan Sashin Creek nan
          SRR1692349 Oct_1-2 Brain nan Sashin Creek nan
          SRR1692354 Oct_21-3 Brain nan Sashin Lake nan
          SRR1692306 Feb_28-2 Brain nan Sashin Lake nan
          SRR1692312 Hatch_74-8 Embryo nan Sashin Creek nan
          SRR1692313 Hatch_106-4 Embryo nan Sashin Lake nan
          SRR1692325 Hatch_107-3 Embryo nan Sashin Lake nan
          SRR1692352 Oct_6-4 Brain nan Sashin Creek nan
          SRR1692360 Oct_29-4 Brain nan Sashin Lake nan
          SRR1692347 June_28-3 Brain nan Sashin Lake nan
          SRR1692353 Oct_20-2 Brain nan Sashin Lake nan
          SRR1692305 Feb_21-5 Brain nan Sashin Lake nan
          SRR1692309 Hatch_66-3 Embryo nan Sashin Creek nan
          SRR1692340 Hatch_117-4 Embryo nan Sashin Lake nan
          SRR1692342 June_2-3 Brain nan Sashin Creek nan
          SRR1692310 Hatch_69-8 Embryo nan Sashin Creek nan
          SRR1692350 Oct_2-2 Brain nan Sashin Creek nan
          SRR1692303 Feb_6-5 Brain nan Sashin Creek nan
  • sex
    • PRJNA380337:
          The study present a chromosome-anchored genome assembly for rainbow trout and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict.
      • key word
        • Sex; ONCORHYNCHUS MYKISS; GENE-EXPRESSION; BALANCING SELECTION; ANTAGONISTIC GENES; WILD POPULATIONS; LINKAGE MAP; SALMON; RECOMBINATION; STEELHEAD; EVOLUTION
      • publication
        • Pearse DE, et al. "Sex-dependent dominance maintains migration supergene in rainbow trout", Nature Ecology & Evolution, 2019; 3:1731-+
      • abstract
        • Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR5373280 Sample_26-RT-Sk-1 Skin nan Sample_26-RT-Sk-1 nan
          SRR5373279 Sample_27-RT-M-1 Muscle nan Sample_27-RT-M-1 nan
          SRR5373271 Sample_35-RT-E-1 Eye nan Sample_35-RT-E-1 nan
          SRR5373274 Sample_32-RT-HK-1 Head kidney nan Sample_32-RT-HK-1 nan
          SRR5373270 Sample_36-RT-B-1 Brain nan Sample_36-RT-B-1 nan
          SRR5373273 Sample_33-RT-Sp-1 Spleen nan Sample_33-RT-Sp-1 nan
          SRR5373277 Sample_29-RT-G-1 Gut nan Sample_29-RT-G-1 nan
          SRR5373278 Sample_28-RT-H-1 Hearth nan Sample_28-RT-H-1 nan
          SRR5373283 Sample_23-RT-L-1 Liver nan Sample_23-RT-L-1 nan
          SRR5373282 Sample_24-24-RT-L-2 Liver nan Sample_24-24-RT-L-2 nan
          SRR5373275 Sample_31-RT-K-1 Kidney nan Sample_31-RT-K-1 nan
          SRR5373276 Sample_30-RT-PC-1 Pyloric caeca nan Sample_30-RT-PC-1 nan
          SRR5373272 Sample_34-RT-Gi-1 Gill nan Sample_34-RT-Gi-1 nan
          SRR5373281 Sample_25-RT-L-3 Liver nan Sample_25-RT-L-3 nan
  • temperature
    • PRJNA448020:
          Transcriptome profiling of rainbow trout head kidney under moderate heat stress
      • key word
        • Temperature; [1]Rainbow trout; Heat stress; RNA-seq; Transcriptome; RNA-SEQ REVEALS; GENE-EXPRESSION; THERMAL-STRESS; TEMPERATURE; FISHES; DEGRADATION; STRATEGIES; DIVERSITY; TRANSPORT; INSIGHTS [2]rainbow trout; hsp90 genes; gene expression pattern; heat stress; SHOCK-PROTEIN; MESSENGER-RNA; PHYLOGENETIC ANALYSIS; FOOD-DEPRIVATION; FAMILY; EVOLUTIONARY; PATTERN; CLONING; GROWTH; CELLS
      • publication
        • [1]Jinqiang, et al. "Transcriptomic responses to heat stress in rainbow trout Oncorhynchus mykiss head kidney. " Fish & Shellfish Immunology (2018). [2]Ma F, et al. "Genome-Wide Identification of hsp90 Gene in Rainbow Trout (Oncorhynchus mykiss) and Their Regulated Expression in Response to Heat Stress", DNA and Cell Biology, 2020; 39:428-440
      • abstract
        • [1]Rainbow trout (Oncorhynchus mykiss) are widely cultured throughout the word for commercial aquaculture. However, as a cold-water species, rainbow trout are highly susceptible to heat stress, which may cause pathological signs or diseases by alleviating the immune roles and then lead to mass mortality. Understanding the molecular mechanisms that occur in the rainbow trout in response to heat stress will be useful to decrease heat stress-related morbidity and mortality in trout aquaculture. In the present study, we conducted transcriptome analysis of head kidney tissue in rainbow trout under heat-stress (24 °C) and control (18 °C) conditions, to identify heat stress-induced genes and pathways. More than 281 million clean reads were generated from six head kidney libraries. Using an adjusted P-value of P < 0.05 as the threshold, a total of 443 differentially expressed genes (DEGs) were identified, including members of the HSP90, HSP70, HSP60, and HSP40 family and several cofactors or cochaperones. The RNA-seq results were confirmed by RT-qPCR. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis of DEGs were performed. Many genes involved in maintaining homeostasis or adapting to stress and stimuli were highly induced in response to high temperature. The most significantly enriched pathway was “Protein processing in endoplasmic reticulum (ER)”, a quality control system that ensures correct protein folding or degradation of misfolded polypeptides by ER-associated degradation. Other signaling pathways involved in regulation of immune system and post-transcriptional regulation of spliceosome were also critical for thermal adaptation. These findings improve our understanding of the molecular mechanisms of heat stress responses and are useful to develop strategies for the improvement of rainbow trout survival rate during summer high-temperature period. [2]In this study, we analyzed the gene structure, chemical characterizations, chromosome locations, evolutionary relationship, and expression profile of hsp90 genes with online database. In addition, the expression levels of hsp90s were also investigated under heat stress by quantitative real-time (qRT)-PCR. A total of eight hsp90 genes were identified from the rainbow trout genome. They were all distributed on chromosomes 2, 4, 8, and 13. The molecular weight ranged from 78.93 to 91.39 kDa, and the isoelectric point ranged from 4.84 to 4.96. The eight hsp90 genes were clustered into six subfamilies (A, B, C, D, E, and F). Genetic structure and conserved domain analysis revealed that all eight hsp90 genes had only one exon, and motif 1-motif 10 was shared by most genes. According to RNA-seq analysis of rainbow trout liver and head kidney, a total of seven out of eight genes were significantly upregulated under heat stress, and qRT-PCR was carried out on these seven genes; the expression levels of these genes were significantly upregulated under heat stress. The significantly regulated expressions of hsp90 genes under heat stress indicated that hsp90 genes are involved in heat stress response in rainbow trout. This study provides a theoretical basis for further study on the role of hsp90 in the heat stress tolerance of rainbow trout.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR6956996 HHK1 head kidney Donaldson strain 44220 nan
          SRR6956998 CHK2 head kidney Donaldson strain 44245 nan
          SRR6956993 HHK2 head kidney Donaldson strain 44251 nan
          SRR6956997 CHK1 head kidney Donaldson strain 44214 nan
          SRR6956995 CHK3 head kidney Donaldson strain 44273 nan
          SRR6956994 HHK3 head kidney Donaldson strain 44279 nan
    • PRJNA352601:
          Transcriptome profiling of rainbow trout liver under moderate heat stress
      • key word
        • Temperature; rainbow trout; hsp90 genes; gene expression pattern; heat stress; SHOCK-PROTEIN; MESSENGER-RNA; PHYLOGENETIC ANALYSIS; FOOD-DEPRIVATION; FAMILY; EVOLUTIONARY; PATTERN; CLONING; GROWTH; CELLS
      • publication
        • Ma F, et al. "Genome-Wide Identification of hsp90 Gene in Rainbow Trout (Oncorhynchus mykiss) and Their Regulated Expression in Response to Heat Stress", DNA and Cell Biology, 2020; 39:428-440
      • abstract
        • In this study, we analyzed the gene structure, chemical characterizations, chromosome locations, evolutionary relationship, and expression profile of hsp90 genes with online database. In addition, the expression levels of hsp90s were also investigated under heat stress by quantitative real-time (qRT)-PCR. A total of eight hsp90 genes were identified from the rainbow trout genome. They were all distributed on chromosomes 2, 4, 8, and 13. The molecular weight ranged from 78.93 to 91.39 kDa, and the isoelectric point ranged from 4.84 to 4.96. The eight hsp90 genes were clustered into six subfamilies (A, B, C, D, E, and F). Genetic structure and conserved domain analysis revealed that all eight hsp90 genes had only one exon, and motif 1-motif 10 was shared by most genes. According to RNA-seq analysis of rainbow trout liver and head kidney, a total of seven out of eight genes were significantly upregulated under heat stress, and qRT-PCR was carried out on these seven genes; the expression levels of these genes were significantly upregulated under heat stress. The significantly regulated expressions of hsp90 genes under heat stress indicated that hsp90 genes are involved in heat stress response in rainbow trout. This study provides a theoretical basis for further study on the role of hsp90 in the heat stress tolerance of rainbow trout.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR4999774 OM_HL3 liver Donaldson strain 44279 nan
          SRR4996863 OM_CL3 liver Donaldson strain 44273 nan
          SRR4996145 OM_CL2 liver Donaldson strain 44245 nan
          SRR4996866 OM_HL1 liver Donaldson strain 44220 nan
          SRR4999772 OM_HL2 liver Donaldson strain 44251 nan
          SRR4996861 OM_CL1 liver Donaldson strain 44214 nan
    • PRJDB3412:
          Different gene expression profiles between normal and thermally selected strains of rainbow trout, Oncorhynchus mykiss, as revealed by comprehensive transcriptome analysis
      • key word
        • Temperature; Oncorhynchus mykiss; Thermally selected strain; Next generation sequencing; Gill;Global gene expression; HSP gene; c-fos gene; HEAT-SHOCK PROTEINS; UPPER TEMPERATURE TOLERANCE; QUANTITATIVE TRAIT LOCI; ONCORHYNCHUS-MYKISS; MOLECULAR CHAPERONES; DNA-SEQUENCES; C-FOS; TRANSCRIPTOME; GENERATION; STRESS
      • publication
        • Tan E et al., "Global gene expression analysis of gill tissues from normal and thermally selected strains of rainbow trout", Fisheries Science, 2012;78(5):1041-1049
      • abstract
        • The objective of the study reported here was to investigate genes related to upper temperature tolerance in rainbow trout Oncorhynchus mykiss, a cold-water species with considerable economic importance, by global gene expression analysis using a next generation sequencing system. Fifty million paired sequences were collected from the gill tissues of each of five individuals of a thermally selected strain developed by selective breeding and from the gilltissues of a standard Donaldson strain and assembled into transcripts. The data of both strains were integrated, and a BLASTX search identified 13,092 independent, known genes. A back-mapping of raw reads from both strains onto the genes, conducted to investigate their frequency of expression, revealed that 324 genes showed at least a twofold higher expression in the thermally selected strain than in the Donaldson strain. In addition, 44.4 % of commonly expressed genes were categorized into 38 functional groups by annotation. Genes encoding heat shock proteins and c-fos-related proteins were highly expressed in the thermally selected strain. Our strategy to employ next generation sequencing proved to be very useful to find genes responsible for upper temperature tolerance of rainbow trout.
      • sample list
        • sample id sample name tissue strain treatment description
          DRR046629 SAMD00041049 Brain nan High-temperature selected strain(HT)_Brain_Before heat exposure nan
          DRR046630 SAMD00041049 Brain nan High-temperature selected strain(HT)_Brain_After heat exposur nan
          DRR046633 SAMD00041049 Heart nan High-temperature selected strain(HT)_Heart_Before heat exposure nan
          DRR046635 SAMD00041049 Muscle nan High-temperature selected strain(HT)_Muscle_Before heat exposure nan
          DRR046636 SAMD00041049 Muscle nan High-temperature selected strain(HT)_Muscle_After heat exposure nan
          DRR046640 SAMD00041048 Brain nan Donaldson strain(DS)_Brain_After heat exposure nan
          DRR046645 SAMD00041048 Muscle nan Donaldson strain(DS)_Muscle_Before heat exposure nan
          DRR046646 SAMD00041048 Muscle nan Donaldson strain(DS)_Muscle_After heat exposure nan
          DRR046639 SAMD00041048 Brain nan Donaldson strain(DS)_Brain_Before heat exposure nan
          DRR046648 SAMD00041048 Gill nan Donaldson strain(DS)_Gill_After heat exposure nan
          DRR046632 SAMD00041049 Liver nan High-temperature selected strain(HT)_Liver_After heat exposure nan
          DRR046644 SAMD00041048 Heart nan Donaldson strain(DS)_Heart_After heat exposure nan
          DRR046634 SAMD00041049 Heart nan High-temperature selected strain(HT)_Heart_After heat exposure nan
          DRR046637 SAMD00041049 Gill nan High-temperature selected strain(HT)_Gill_Before heat exposure nan
          DRR046638 SAMD00041049 Gill nan High-temperature selected strain(HT)_Gill_After heat exposure nan
          DRR046647 SAMD00041048 Gill nan Donaldson strain(DS)_Gill_Before heat exposure nan
          DRR046641 SAMD00041048 Liver nan Donaldson strain(DS)_Liver_Before heat exposure nan
          DRR046642 SAMD00041048 Liver nan Donaldson strain(DS)_Liver_After heat exposure nan
          DRR046643 SAMD00041048 Heart nan Donaldson strain(DS)_Heart_Before heat exposure nan
          DRR046631 SAMD00041049 Liver nan High-temperature selected strain(HT)_Liver_Before heat exposure nan
    • PRJNA559610:
          Identification and analysis of long non-coding RNAs reveals regulatory mechanisms responses to heat stress in rainbow trout (Oncorhynchus mykiss) (rainbow trout)
      • key word
        • Temperature; [1]Rainbow trout; Heat stress; Transcriptome; ceRNA network; [2]Rainbow trout; Heat stress; Long noncoding RNAs; Transcriptome; SHOCK PROTEINS; POTENTIAL ROLE; B2 RNA; MECHANISMS; LNCRNAS; TRANSCRIPTION; PREDICTION; LANDSCAPE; DISCOVERY; EVOLUTION
      • publication
        • [1]Quan, J. , et al. "Integrated analysis of the responses of a circRNA-miRNA-mRNA ceRNA network to heat stress in rainbow trout (Oncorhynchus mykiss) liver." BMC Genomics 22.1(2021). [2]Quan, J. , et al. "Identification and characterization of long noncoding RNAs provide insight into the regulation of gene expression in response to heat stress in rainbow trout (Oncorhynchus mykiss)." Comparative Biochemistry and Physiology Part D Genomics and Proteomics 36(2020):100707.
      • abstract
        • [1]Background: With the intensification of global warming, rainbow trout (Oncorhynchus mykiss) suffer from varying degrees of thermal stimulation, leads to mass mortality, which severely restrict thedevelopment of aquaculture. Understanding the molecular regulatory mechanisms of rainbow troutunder heat stress is useful to develop approaches to relieve symptoms. Results: Changes in nonspecific immune parameters revealed that a strong stress response was caused in rainbow trout at 24 degrees C, so we performed multiple transcriptomic analyses of rainbow trout liver under heat stress (HS, 24 degrees C) and control conditions (CG, 18 degrees C). A total of 324 DEcircRNAs, 105 DEmiRNAs, and 1885 DEmRNAs were identified. A ceRNA regulatory network was constructed and a total of 301 circRNA-miRNA and 51 miRNA-mRNA negative correlation pairs were screened, and three regulatory correlation pairs were predicted: novel_circ_003889 - novel-m0674-3p - hsp90ab1, novel_circ_002325 - miR-18-y - HSPA13 and novel_circ_002446 - novel-m0556-3p - hsp70. Some target genes involved in metabolic processes, biological regulation or response to stimulus were highly induced at high temperatures. Several important pathways involved in heat stress were characterized, such as protein processing in the ER, the estrogen signaling pathway, and the HIF-1 signaling pathway. Conclusions: These results extend our understanding of the molecular mechanisms of the heat stress response and provide novel insight for the development of strategies that relieve heat stress. [2]Rainbow trout are typical cold-water fish species. However, with the intensification of global warming, high temperatures have severely restricted the development of aquaculture during the summer. Understanding the molecular regulatory mechanisms of rainbow trout responses to heat stress will be beneficial for alleviating heat stress-related damage. In this study, we performed RNA-seq of liver tissues from rainbow trout under heat stress (24 degrees C) and control conditions (18 degrees C) to identify lncRNAs and target genes by strand-specific library. Changes in nonspecific immune parameters revealed that a strong stress response occurred in rainbow trout at 24 degrees C. More than 658 million filtered reads and 5916 lncRNAs were identified from six libraries. A total of 927 novel lncRNAs were identified, and 428 differentially expressed lncRNAs were screened with stringent thresholds. The RNA-seq results were verified by RT-qPCR. In addition, a regulatory network of lncRNA-mRNA functional interactions was constructed, and the potential antisense, cis and trans targets of lncRNAs were predicted. GO and KEGG enrichment analyses showed that many target genes involved in maintenance of homeostasis or adaptation to stress and stimuli were highly induced under heat stress. Several regulatory pathways were also found to be involved in heat stress, including the thyroid hormone signaling pathway, the PI3K-Akt signaling pathway, and the estrogen signaling pathway, among others. These results broaden our understanding of lncRNAs associated with heat stress and provide new insights into the lncRNA mediated regulation of the rainbow trout heat stress response.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR9943833 GSM4025692 liver nan control nan
          SRR9943834 GSM4025693 liver nan control nan
          SRR9943835 GSM4025694 liver nan control nan
          SRR9943836 GSM4025695 liver nan under heat stress nan
          SRR9943837 GSM4025696 liver nan under heat stress nan
          SRR9943838 GSM4025697 liver nan under heat stress nan
  • vaccine
    • PRJNA530387:
          Ig repertoire of Fish vaccinated against VHSV and infected by IPNV
      • key word
        • Vaccine, VHSV, IPNV, antibodies, B cell repertoire, heterologous immunization, public response, fish immunology, RepSeq, comparative immunology
      • publication
        • Navelsaker, S. , et al. "Sequential Immunization With Heterologous Viruses Does Not Result in Attrition of the B Cell Memory in Rainbow Trout." Frontiers in Immunology (2019):2687.
      • abstract
        • Long-term immunity is of great importance for protection against pathogens and has been extensively studied in mammals. Successive heterologous infections can affect the maintenance of immune memory, inducing attrition of T memory cells and diminishing B cell mediated protection. In fish, the basis of immune memory and the mechanisms of immunization to heterologous pathogens remain poorly understood. We sequentially immunized isogenic rainbow trout with two immunologically distinct viruses, VHSV and IPNV, either with one virus only or in combination, and analyzed the antibody responses and repertoires. Neutralizing antibodies and ELISPOT did not reveal an effect of heterologous immunization. Using a consensus read sequencing approach that incorporates unique barcodes to each cDNA molecule, we focused on the diversity expressed by selected responding VH/C combinations. We identified both public and private responses against VHSV and/or IPNV in all groups of fish. In fish immunized with two viruses, we registered no significant reduction in the persistence of the response toward the primary immunization. Similarly, the response to the second immunization was not affected by a prior vaccination to the other virus. Our data suggest that heterologous immunization does not enforce attrition of pre-existing antibody producing cells, which may impair the protection afforded by multiple successive vaccinations. These observations are potentially important to improve vaccination strategies practiced in aquaculture.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR8835976 5B3 spleen Isogenic line B57 Fish vaccinated agains VHSV and infected by IPNV nan
          SRR8835982 7.3 spleen Isogenic line B57 Fish infected by IPNV nan
          SRR8835975 5B4 spleen Isogenic line B57 Fish vaccinated agains VHSV and infected by IPNV nan
          SRR8835979 7.2 spleen Isogenic line B57 Fish infected by IPNV nan
          SRR8835977 5B1 spleen Isogenic line B57 Fish vaccinated agains VHSV and infected by IPNV nan
          SRR8835981 7.4 spleen Isogenic line B57 Fish infected by IPNV nan
          SRR8835971 5B8 spleen Isogenic line B57 Fish vaccinated agains VHSV, infected by IPNV, then boosted by VHSV nan
          SRR8835972 5B7 spleen Isogenic line B57 Fish vaccinated agains VHSV, infected by IPNV, then boosted by VHSV nan
          SRR8835974 5B5 spleen Isogenic line B57 Fish vaccinated agains VHSV, infected by IPNV, then boosted by VHSV nan
          SRR8835973 5B6 spleen Isogenic line B57 Fish vaccinated agains VHSV, infected by IPNV, then boosted by VHSV nan
          SRR8835980 7.1 spleen Isogenic line B57 Fish infected by IPNV nan
          SRR8835978 5A3 spleen Isogenic line B57 Fish vaccinated agains VHSV and infected by IPNV nan
    • PRJDB6875:
          mRNA seq of UEA-1+ Ass+ and UEA-1- Ass+ antigen sampling cells
      • key word
        • Vaccine; Aeromonas salmonicida subsp salmonicida, gill epithelium, bacterin, antigen
      • publication
        • nan
      • abstract
        • We aimed to characterize antigen sampling cells which uptake Aeromonas salmonicida subsp salmonicida (Ass) bacterin in the gill epithelium of rainbow trout. There are two phenotypes of the antigen sampling cells in the gill epithelium: UEA-1+Ass+ and UEA-1-Ass+ cells. We sorted the three cell fractions (UEA-1+Ass+, UEA-1-Ass+ and totally negative) from gill-epithelial cells of fish bath-vaccinated with Ass bacterin.
      • sample list
        • sample id sample name tissue strain treatment description
          DRR127912 SAMD00115100 UEA-1+Ass+ cells Aeromonas salmonicida subsp salmonicida (Ass) mRNA seq of UEA-1+Ass+ cells nan
          DRR127913 SAMD00115101 UEA-1-Ass+ cells Aeromonas salmonicida subsp salmonicida (Ass) mRNA seq of UEA-1-Ass+ cells nan
          DRR127914 SAMD00115102 negative cells Aeromonas salmonicida subsp salmonicida (Ass) mRNA seq of negative cells nan

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