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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
    • PRJNA448819:
          The striped catfish (Pangasianodon hypophthalmus), which belongs to Pangasiidae family, is native to Mekong river (Vietnam, Cambodia, Lao and Thailand). The species is successfully cultured, especially in the Mekong river delta. The present study provides high-quality genomic information of P. hypophthalmus for future studies of aquaculture of striped catfish in South-Eastern Asia. These genomic data are useful for further improvement in aquaculture of the striped catfish in this area.
      • key word
        • baseline;Striped catfish;Draft nuclear genome;Gadusol biosynthetic genes;Vitamin D-binding protein;cPLA2;Hox cluster;IGF;MHCI;Sex-determination genes;Hypothetical chromosome;INFECTIOUS PANCREATIC NECROSIS;MULTIPLE SEQUENCE ALIGNMENT;PROVIDES INSIGHTS;GROWTH;ANNOTATION;EVOLUTION;FISH;CLUSTERS;PROTEIN;MEDAKA
      • publication
        • Kim OTP et al., "A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement.", BMC Genomics, 2018 Oct 5;19(1):733
      • abstract
        • Background:The striped catfish, Pangasianodon hypophthalmus, is a freshwater and benthopelagic fish common in the Mekong River delta. Catfish constitute a valuable source of dietary protein. Therefore, they are cultured worldwide, and P. hypophthalmus is a food staple in the Mekong area. However, genetic information about the culture stock, is unavailable for breeding improvement, although genetics of the channel catfish, Ictalurus punctatus, has been reported. To acquire genome sequence data as a useful resource for marker-assisted breeding, we decoded a draft genome of P. hypophthalmus and performed comparative analyses.Results:Using the Illumina platform, we obtained both nuclear and mitochondrial DNA sequences. Molecular phylogeny using the mitochondrial genome confirmed that P. hypophthalmus is a member of the family Pangasiidae and is nested within a clade including the families Cranoglanididae and Ictaluridae. The nuclear genome was estimated at approximately 700 Mb, assembled into 568 scaffolds with an N50 of 14.29 Mbp, and was estimated to contain ~ 28,600 protein-coding genes, comparable to those of channel catfish and zebrafish. Interestingly, zebrafish produce gadusol, but genes for biosynthesis of this sunscreen compound have been lost from catfish genomes. The differences in gene contents between these two catfishes were found in genes for vitamin D-binding protein and cytosolic phospholipase A2, which have lost only in channel catfish. The Hox cluster in catfish genomes comprised seven paralogous groups, similar to that of zebrafish, and comparative analysis clarified catfish lineage-specific losses of A5a, B10a, and A11a. Genes for insulin-like growth factor (IGF) signaling were conserved between the two catfish genomes. In addition to identification of MHC class I and sex determination-related gene loci, the hypothetical chromosomes by comparison with the channel catfish demonstrated the usefulness of the striped catfish genome as a marker resource.Conclusions:We developed genomic resources for the striped catfish. Possible conservation of genes for development and marker candidates were confirmed by comparing the assembled genome to that of a model fish, Danio rerio, and to channel catfish. Since the catfish genomic constituent resembles that of zebrafish, it is likely that zebrafish data for gene functions is applicable to striped catfish as well.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR6943526 Striped catfish zygote nan untreatment zygote
          SRR6943527 Striped catfish brain nan untreatment brain
          SRR6943528 Striped catfish morula nan untreatment morula
          SRR6943529 Striped catfish 4-cell stage nan untreatment 4-cell stage
          SRR6943530 Striped catfish heart nan untreatment heart
          SRR6943531 Striped catfish kidney nan untreatment kidney
          SRR6943532 Striped catfish fins nan untreatment fins
          SRR6943533 Striped catfish gill nan untreatment gill
          SRR6943534 Striped catfish gastrula nan untreatment gastrula
          SRR6943535 Striped catfish blastula nan untreatment blastula
          SRR6943536 Striped catfish closing of the blastopore nan untreatment closing of the blastopore
          SRR6943537 Striped catfish development of tail and head buds nan untreatment development of tail and head buds
          SRR6943538 Striped catfish egg ready for hatching nan untreatment egg ready for hatching
          SRR6943539 Striped catfish freshly hatched larvae nan untreatment freshly hatched larvae
          SRR6943540 Striped catfish one-day old larvae nan untreatment one-day old larvae
          SRR6943541 Striped catfish two-day old larvae nan untreatment two-day old larvae
          SRR6943542 Striped catfish liver nan untreatment liver
          SRR6943543 Striped catfish muscle nan untreatment muscle
          SRR6943544 Striped catfish spleen nan untreatment spleen
          SRR6943545 Striped catfish male testis nan untreatment male testis
    • PRJNA256963:
          Transcriptome analysis of 11 panga tissues
      • key word
        • baseline;Gene duplication;TeleostsHolostean;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 17.1(2016):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 whole genome 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 fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish 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 the evolution 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
          SRR1533640 G_Ph_1 ovary nan untreatment Panga ovary
          SRR1533641 G_Ph_2 brain nan untreatment Panga brain
          SRR1533642 G_Ph_3 gill nan untreatment Panga gills
          SRR1533643 G_Ph_4 heart nan untreatment Panga heart
          SRR1533644 G_Ph_5 muscle nan untreatment Panga muscle
          SRR1533645 G_Ph_6 liver nan untreatment Panga liver
          SRR1533646 G_Ph_7 head kidney nan untreatment Panga kidney
          SRR1533647 G_Ph_8 bones nan untreatment Panga bones
          SRR1533648 G_Ph_9 intestine nan untreatment Panga intestine
          SRR1533649 G_Ph_10 testis nan untreatment Panga testis
          SRR1533650 G_Ph_11 embryos nan untreatment Panga embryo
  • low oxygen
    • PRJNA647859:
          Channel catfish (Ictalurus punctatus) and tra catfish (Pangasianodon hypophthalmus) both belong to the order Siluriformes. Channel catfish does not possess an air-breathing organ (ABO), and thus cannot breathe in the air, while tra catfish is a facultative air-breather and use the swim bladder as its air-breathing organ, which provides for aerial breathing in low oxygen conditions. Tra and channel catfish serve as a great comparative model for studying the transition of life from water to terrestrial living, as well as for understanding genes that are crucial for development of the swim bladder and the function of air-breathing in tra catfish. We selected seven developmental stages in tra catfish for RNA-Seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated in tra catfish, and a total of 21, 448 unique genes were detected. A comparative genomic analysis was conducted between channel catfish and tra catfish. Gene expression analysis was performed for these tra catfish specific genes. Hypoxia challenge and microtomy experiments collectively suggested that there are critical timepoints for the development of the air-breathing function and swim bladder development stages in tra catfish. Key genes were identified to be the best candidates of genes related to the air-breathing ability in tra catfish. This study provides a large data resource for functional genomic studies in air-breathing function in tra catfish, and sheds light on the adaption of aquatic organisms to the terrestrial environment. Overall design: Profile of transcriptome-wide gene expression levels in seven early development stages of Pangasianodon hypophthalmus
      • key word
        • low oxygen;air-breathing, mRNA-seq, tra catfish, terrestrial adaptation, low-oxygen tolerance
      • publication
        • Ma X et al., "Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation.", Front Genet, 2020;11:608325
      • abstract
        • Tra catfish (Pangasianodon hypophthalmus), also known as striped catfish, is a facultative air-breather that uses its swim bladder as an air-breathing organ (ABO). A related species in the same order (Siluriformes), channel catfish (Ictalurus punctatus), does not possess an ABO and thus cannot breathe in the air. Tra and channel catfish serve as great comparative models for investigating possible genetic underpinnings of aquatic to land transitions, as well as for understanding genes that are crucial for the development of the swim bladder and the function of air-breathing in tra catfish. In this study, hypoxia challenge and microtomy experiments collectively revealed critical time points for the development of the air-breathing function and swim bladder in tra catfish. Seven developmental stages in tra catfish were selected for RNA-seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated, and a total of 21,448 unique genes were detected. A comparative genomic analysis between channel catfish and tra catfish revealed 76 genes that were present in tra catfish, but absent from channel catfish. In order to further narrow down the list of these candidate genes, gene expression analysis was performed for these tra catfish-specific genes. Fourteen genes were inferred to be important for air-breathing. Of these, HRG, GRP, and CX3CL1 were identified to be the most likely genes related to air-breathing ability in tra catfish. This study provides a foundational data resource for functional genomic studies in air-breathing function in tra catfish and sheds light on the adaptation of aquatic organisms to the terrestrial environment.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR12287823 GSM4682421 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 2dpf_rep1
          SRR12287824 GSM4682422 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 2dpf_rep2
          SRR12287825 GSM4682423 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 4dpf_rep1
          SRR12287826 GSM4682424 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 4dpf_rep2
          SRR12287827 GSM4682425 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 6dpf_rep1
          SRR12287828 GSM4682426 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 6dpf_rep2
          SRR12287829 GSM4682427 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 8dpf_rep1
          SRR12287830 GSM4682428 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 8dpf_rep2
          SRR12287831 GSM4682429 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 9dpf_rep1
          SRR12287832 GSM4682430 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 9dpf_rep2
          SRR12287833 GSM4682431 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 10dpf_rep1
          SRR12287834 GSM4682432 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 10dpf_rep2
          SRR12287835 GSM4682433 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 11dpf_rep1
          SRR12287836 GSM4682434 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 11dpf_rep2

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