OVERVIEW


FishGET is an evolutionarily-supported database of species covering two whole genome duplication (WGD) events. We committed to collect and organize a large number of pair-end data of ray-finned fish for unified analysis, which will lead to more complete reference transcriptome, and provided gene / RNA expression profile in different experiment type and tissues during the entire development. The figure on the right shows the overview of the data analysis process.

Cite: Cheng Guo, You Duan, Weidong Ye et al. FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization. iScience. 10.1016/j.isci.2023.106539.




RELATED SPECIES

FishGET covers 8 species, which are classified into model, economic, ornamental and ornamental fish according to several article introduction.

DATA SOURCE

We downloaded 97 bioprojects from SRA and GSA, of which 93 were used for analysis and 4 used for article information storage only.

EXPERIMENT TYPE

We manually classified 97 bioprojects according to experiment types (eg: baseline: 32 bioprojects). And we organized the relevant information of 79 articles.

TRANSCRIPTOME

About 55% gene / RNA come from the genome GTF file, and about 45% non-coding gene / lncRNA come from the FishGET assembly pipeline.

EXPRESSION PROFILE

93 bioprojects cover 1317 samples. Users can perform cross-bioproject visualizations for comparative analysis.

ANNOTATION

Including co-expression network, NR / KEGG / GO, neighboring location, lncRNA type identification and homologous annotation.


DISTRIBUTION OF BIOPROJECTS

The phylogenetic relationships among the ray-finned fishes in FishGET are shown in the figure below left. This 8 fishes span two different whole genome duplication events found in teleost fish. Including teleost-specific WGD event (the first red star) and salmonid-specific WGD event (the second red star).

The distribution of bioprojects in FishGET is shown in the following figure on the right. The number of bioprojects and samples of each species are shown in the stacked bar figure, and the experiment types covered by each species are shown in the pie figure.



BASIC INFORMATION OF SPECIES

  ornamental fish

  Genome version: AmiCal1
  Transcriptome source:
      > FishGET assembly       > NCBI(GenBank assembly)
   Bioproject source: NCBI(SRA)

 bowfin (Amia calva)

Classification:
Actinopteri (ray-finned fishes) > Amiiformes (Bowfins) > Amiidae (Bowfins)   Skip to FishBase

  ornamental fish

  Genome version: ASM1883169v1
  Transcriptome source:
      > FishGET assembly       > NCBI(RefSeq assembly)
  Bioproject source: NCBI(SRA)

 tiger barb (Puntius tetrazona)

Classification:
Actinopteri (ray-finned fishes) > Cypriniformes (Carps) > Cyprinidae (Minnows or carps) > Smiliogastrinae   Skip to FishBase

  economic fish

  Genome version:
      v1_2015/06_NatureGenetics
  Transcriptome source:
      FishGET assembly
  Bioproject source:
      > NCBI(SRA)
      > GSA

 grass carp (Ctenopharyngodon idella)

Classification:
Actinopteri (ray-finned fishes) > Cypriniformes (Carps) > Xenocyprididae (East Asian minnows)   Skip to FishBase

  model fish

  Genome version: GRCz11
  Transcriptome source:
      > ensembl
      > LncRBase V.2
      > ZFLNC
  Bioproject source:
       NCBI: (PRJEB12982)

 zebrafish (Danio rerio)

Classification:
Actinopteri (ray-finned fishes) > Cypriniformes (Carps) > Danionidae (Danios) > Danioninae   Skip to FishBase

  ornamental fish

  Genome version:
      Astyanax_mexicanus-2.0
  Transcriptome source:
      > FishGET assembly       > NCBI(RefSeq assembly)
  Bioproject source: NCBI(SRA)

 mexican tetra (Astyanax mexicanus)

Classification:
Actinopteri (ray-finned fishes) > Characiformes (Characins) > Characidae (Characins; tetras) > Stethaprioninae   Skip to FishBase

  economic fish

  Genome version: GENO_Phyp_1.0
  Transcriptome source:
      > FishGET assembly       > NCBI(RefSeq assembly)
  Bioproject source: NCBI(SRA)

 striped catfish (Pangasianodon hypophthalmus)

Classification:
Actinopteri (ray-finned fishes) > Siluriformes (Catfishes) > Pangasiidae (Shark catfishes)   Skip to FishBase

  economic fish

  Genome version:
     USDA_OmykA_1.1
  Transcriptome source:
      > FishGET assembly       > NCBI(RefSeq assembly)
  Bioproject source: NCBI(SRA)

 rainbow trout (Oncorhynchus mykiss)

Classification:
Actinopteri (ray-finned fishes) > Salmoniformes (Salmons) > Salmonidae (Salmonids) > Salmoninae   Skip to FishBase

  economic fish

  Genome version: GENO_Pfluv_1.0
  Transcriptome source:
      > FishGET assembly       > NCBI(RefSeq assembly)
  Bioproject source: NCBI(SRA)

 eurasian perch (Perca fluviatilis)

Classification:
Actinopteri (ray-finned fishes) > Perciformes/Percoidei (Perchs) > Percidae (Perches) > Percinae   Skip to FishBase


 zebrafish

(Danio rerio)

 model fish


 grass carp

(Ctenopharyngodon idella)

 economic fish


 rainbow trout

(Oncorhynchus mykiss)

 economic fish


 eurasian perch

(Perca fluviatilis)

 economic fish


 striped catfish

(Pangasianodon hypophthalmus)

 economic fish


 bowfin

(Amia calva)

 ornamental fish


 tiger barb

(Puntius tetrazona)

 ornamental fish


 mexican tetra

(Astyanax mexicanus)

 ornamental fish




 DATA SOURCES