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Plant Genome DataBase Japan (PGDBj).

Akihiro Nakaya1, Hisako Ichihara2, Erika Asamizu3

  • 1Department of Genome Informatics, Graduate School of Medicine, Osaka University, 1-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.

Methods in Molecular Biology (Clifton, N.J.)
|December 18, 2016
PubMed
Summary
This summary is machine-generated.

The Plant Genome DataBase Japan (PGDBj) integrates diverse plant genomic data, offering a unified platform for researchers. This resource facilitates fundamental and applied studies across numerous plant species.

Keywords:
DNA markerOrthologPGDBjPlant bioresourcePlant genomics

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Genomic and bio-resource information for plants is often fragmented across various databases and literature.
  • Efficient access to integrated plant genomic data is crucial for both fundamental research and agricultural applications.

Purpose of the Study:

  • To develop a comprehensive portal website, the Plant Genome DataBase Japan (PGDBj), for integrating diverse plant genomic information.
  • To provide a seamless search experience across multiple specialized databases and resources.

Main Methods:

  • Developed PGDBj with three core component databases: Ortholog DB, Plant Resource DB, and DNA Marker DB.
  • Integrated over 1,000,000 amino acid sequences from 40 Viridiplantae species for ortholog clustering using reciprocal BLAST searches.
  • Incorporated data from public DNA databases, plant genome databases (TAIR, RAP-DB), SABRE DB, and RIKEN BioResource Center.

Main Results:

  • Established PGDBj, a unified platform featuring an Ortholog DB for gene cluster analysis, a Plant Resource DB for genomic and bio-resources, and a DNA Marker DB for genetic information.
  • Implemented a cross-search engine for efficient querying across all integrated component databases.
  • Collected and curated extensive data, including over a million amino acid sequences and detailed information on DNA markers, QTLs, and genetic maps.

Conclusions:

  • PGDBj serves as a valuable, integrated platform for studying plant genetic systems.
  • The database supports both fundamental and applied research across a wide array of plant species.
  • Facilitates easier access to and analysis of plant genomic and genetic resources.