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Related Experiment Video

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DNA-based Fish Species Identification Protocol
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FishDB: an integrated functional genomics database for fishes.

Liandong Yang1, Zetan Xu2, Honghui Zeng1

  • 1State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.

BMC Genomics
|November 18, 2020
PubMed
Summary
This summary is machine-generated.

FishDB is the first database for fish multi-level omics data, integrating genomes, transcriptomes, and regulatory RNAs. This resource enhances fish genomic research with comprehensive, searchable data.

Keywords:
AdaptationEvolutionFishGenomeTranscriptome

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Area of Science:

  • Genomics
  • Bioinformatics
  • Ichthyology

Background:

  • Numerous fish genomes and transcriptomes have been sequenced recently.
  • Existing fish genomic data lacks a unified, comprehensive, and current collection.

Purpose of the Study:

  • To establish the first database for fish multi-level omics data.
  • To provide an integrated and accessible platform for fish genomic resources.

Main Methods:

  • Data compilation and integration of existing fish genomic and transcriptomic datasets.
  • Generation of new fish genome and transcriptome data.
  • Development of a web-accessible database with search functionalities.

Main Results:

  • FishDB hosts 233 fish genomes, 201 transcriptomes, 5841 mitochondrial genomes, 88 gene sets, and extensive small RNA data (miRNAs, piRNAs, lncRNAs).
  • Includes over 59,040 Mb of untranslated regions (UTR) and 31,918 Mb of coding sequences (CDS) for 230 fish species.
  • Newly generated data includes 11 fish genomes and 53 fish transcriptomes.

Conclusions:

  • The initial release of FishDB contains over 410,721.67 Mb of sequence data.
  • Provides essential bioinformatics tools including search functionality, a BLAST server, JBrowse, and PrimerServer.
  • Establishes a foundational resource for advancing fish genomics and related research.