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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
    • PRJNA684636:
          We performed the genome sequencing of Puntius tetrazona using Nanopore, Illumina and HiC technologies and generate a chromosome-level assembly. Using transcriptome sequencing from multiple tissues, we predicted protein-coding genes of this species.
      • key word
        • baseline;GENETIC DIVERSITY;PROVIDES INSIGHTS;MODEL SELECTION;GENOME SEQUENCE;READ ALIGNMENT;POLYPLOIDY;ORIGIN;ANNOTATION;RECONSTRUCTION;FRACTIONATION
      • publication
        • Jiong-Tang, L. , et al. "Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish." Nature Genetics.
      • abstract
        • Genomic analysis of allo-tetraploid common carp and goldfish identifies parallel subgenome structure and divergent expression processes. How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR13356954 liver liver nan untreatment liver RNA-seq replicate 1
          SRR13356955 muscle muscle nan untreatment muscle RNA-seq replicate 3
          SRR13356956 muscle muscle nan untreatment muscle RNA-seq replicate 2
          SRR13356959 muscle muscle nan untreatment muscle RNA-seq replicate 1
          SRR13356960 skin skin nan untreatment skin RNA-seq replicate 3
          SRR13356961 skin skin nan untreatment skin RNA-seq replicate 2
          SRR13356962 skin skin nan untreatment skin RNA-seq replicate 1
          SRR13356963 spleen spleen nan untreatment spleen RNA-seq replicate 3
          SRR13356964 spleen spleen nan untreatment spleen RNA-seq replicate 2
          SRR13356965 spleen spleen nan untreatment spleen RNA-seq replicate 1
          SRR13356966 brain brain nan untreatment brain RNA-seq replicate 3
          SRR13356967 brain brain nan untreatment brain RNA-seq replicate 2
          SRR13356968 brain brain nan untreatment brain RNA-seq replicate 1
          SRR13356969 gill gill nan untreatment gill RNA-seq replicate 3
          SRR13356970 gill gill nan untreatment gill RNA-seq replicate 2
          SRR13356971 gill gill nan untreatment gill RNA-seq replicate 1
          SRR13356972 heart heart nan untreatment Heart RNA-seq replicate 3
          SRR13356973 heart heart nan untreatment Heart RNA-seq replicate 2
          SRR13356974 heart heart nan untreatment Heart RNA-seq replicate 1
          SRR13356975 intestine intestine nan untreatment intestine RNA-seq replicate 3
          SRR13356977 intestine intestine nan untreatment intestine RNA-seq replicate 2
          SRR13356978 intestine intestine nan untreatment intestine RNA-seq replicate 1
          SRR13356979 kidney kidney nan untreatment kidney RNA-seq replicate 3
          SRR13356980 kidney kidney nan untreatment kidney RNA-seq replicate 2
          SRR13356981 kidney kidney nan untreatment kidney RNA-seq replicate 1
          SRR13356982 liver liver nan untreatment liver RNA-seq replicate 3
          SRR13356983 liver liver nan untreatment liver RNA-seq replicate 2
  • temperature
    • PRJNA478787:
          tiger barb Raw sequence reads
      • key word
        • temperature;Cold stress;Multiple tissues;Tropical stenothermal fish;Ubiquitin-mediated protein degradation;Heat shock 70 KDa protein;Cold-induced RNA-binding protein;RNA-BINDING PROTEIN;TILAPIA OREOCHROMIS-NILOTICUS;DIFFERENTIAL GENE-EXPRESSION;HSP70 MESSENGER-RNA;HEAT-SHOCK RESPONSE;GILTHEAD SEA BREAM;NILE TILAPIA;PHYSIOLOGICAL-RESPONSES;THERMAL-STRESS;COMMON CARP
      • publication
        • Liu, Lili , et al. "Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb ( Puntius tetrazona )." BMC Genomics 21.1(2020).
      • abstract
        • Background Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. The tiger barb Puntius tetrazona is a tropical stenothermal fish, with great popularity in aquarium trade and research. Results To investigate the response mechanism of P. tetrazona to low temperature, fish were exposed to increasing levels of acute cold stress. Histopathological analysis showed that the brain, gill, liver and muscle tissues appeared serious damage after cold stress (13 degrees C). Brain, gill, liver and muscle tissues from control (CTRL) groups (27 degrees C) and COLD stress groups (13 degrees C) of eight-month fish (gender-neutral) were sampled and assessed for transcriptomic profiling by high-throughput sequencing. 83.0 Gb of raw data were generated, filtered and assembled for de novo transcriptome assembly. According to the transcriptome reference, we obtained 392,878 transcripts and 238,878 unigenes, of which 89.29% of the latter were annotated. There were 23,743 differently expressed genes (DEGs) been filtered from four pairs of tissues (brain, gill, liver and muscle) between these cold stress and control groups. These DEGs were mainly involved in circadian entrainment, circadian rhythm, biosynthesis of steroid and fatty acid. There were 64 shared DEGs between the four pairs of groups, and five were related to ubiquitylation/deubiquitylation. Our results suggested that ubiquitin-mediated protein degradation might be necessary for tropical stenothermal fish coping with acute cold stress. Also, the significant cold-induced expression of heat shock 70 kDa protein (HSP70) and cold-induced RNA-binding protein (CIRBP) was verified. These results suggested that the expression of the molecular chaperones HSP70 and CIRBP in P. tetrazona might play a critical role in coping with acute cold stress. Conclusions This is the first transcriptome analysis of P. tetrazona using RNA-Seq technology. Novel findings about tropical stenothermal fish under cold stress (such as HSP70 and CIRBP genes) are presented here. This study contributes new insights into the molecular mechanisms of tropical stenothermal species response to acute cold stress.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR7507732 27muscleB muscle nan 27C RNA-seq of tiger barb: adult muscle-27C
          SRR7507733 27liverD liver nan 27C RNA-seq of tiger barb: adult liver-27C
          SRR7507734 27gillA gill nan 27C RNA-seq of tiger barb: adult gill-27C
          SRR7507735 27brainC brain nan 27C RNA-seq of tiger barb: adult brain-27C
          SRR7507736 27brainB brain nan 27C RNA-seq of tiger barb: adult brain-27C
          SRR7507737 27brainA brain nan 27C RNA-seq of tiger barb: adult brain-27C
          SRR7507738 27liverB liver nan 27C RNA-seq of tiger barb: adult liver-27C
          SRR7507739 27liverA liver nan 27C RNA-seq of tiger barb: adult liver-27C
          SRR7507740 27gillC gill nan 27C RNA-seq of tiger barb: adult gill-27C
          SRR7507741 27gillB gill nan 27C RNA-seq of tiger barb: adult gill-27C
          SRR7507742 13liverC liver nan 13C RNA-seq of tiger barb: adult liver-13C
          SRR7507743 13muscleA muscle nan 13C RNA-seq of tiger barb: adult muscle-13C
          SRR7507744 13muscleB muscle nan 13C RNA-seq of tiger barb: adult muscle-13C
          SRR7507745 13muscleC muscle nan 13C RNA-seq of tiger barb: adult muscle-13C
          SRR7507746 13liverB liver nan 13C RNA-seq of tiger barb: adult liver-13C
          SRR7507747 13liverA liver nan 13C RNA-seq of tiger barb: adult liver-13C
          SRR7507748 27muscleD muscle nan 27C RNA-seq of tiger barb: adult muscle-27C
          SRR7507749 27muscleC muscle nan 27C RNA-seq of tiger barb: adult muscle-27C
          SRR7507750 13brainB brain nan 13C RNA-seq of tiger barb: adult brain-13C
          SRR7507751 13brainA brain nan 13C RNA-seq of tiger barb: adult brain-13C
          SRR7507752 13gillA gill nan 13C RNA-seq of tiger barb: adult gill-13C
          SRR7507753 13brainC brain nan 13C RNA-seq of tiger barb: adult brain-13C
          SRR7507754 13gillC gill nan 13C RNA-seq of tiger barb: adult gill-13C
          SRR7507755 13gillB gill nan 13C RNA-seq of tiger barb: adult gill-13C

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Gene / RNA

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gene ID

RNA ID

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copyright 2021-present@Lab of Aquatic Bioinfomatics, Institute of Hydrobiology, Chinese Academy of Sciences