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OryGenesDB: a database for rice reverse genetics.

G Droc1, M Ruiz, P Larmande

  • 1CIRAD, UMR PIA 1096 TA, 40/03 Avenue Agropolis, 34398 Montpellier Cedex 5, France.

Nucleic Acids Research
|December 31, 2005
PubMed
Summary
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OryGenesDB is a new database for rice functional genomics, cataloging 44,166 insertion mutants using Flanking Sequence Tags (FSTs). It aids researchers in identifying gene insertions and facilitates comparative genomics between rice and Arabidopsis.

Area of Science:

  • Plant genomics
  • Functional genomics
  • Bioinformatics

Background:

  • Insertional mutant databases with Flanking Sequence Tags (FSTs) are crucial for plant functional genomics.
  • Rice (Oryza sativa) is a model organism for cereal crop research.

Purpose of the Study:

  • To develop OryGenesDB, a dedicated database for rice reverse genetics.
  • To provide a comprehensive resource for accessing and analyzing rice insertion mutant data.

Main Methods:

  • Cataloging 44,166 Flanking Sequence Tags (FSTs) from rice insertional mutagenesis projects.
  • Utilizing the Generic Genome Browser (GGB) for the OryGenesDB genome browser.
  • Implementing search functionalities including BLAST, keywords, and gene name searches.
  • Integrating an 'anchoring' option for mapping nucleic acid sequences.

Related Experiment Videos

  • Linking rice and Arabidopsis genomes via predicted orthologs using Best BLAST Mutual Hit (BBMH).

    • Main Results:

    • OryGenesDB houses 44,166 FSTs, providing extensive data on rice gene insertions.
    • The database offers robust search and analysis tools for identifying gene insertion positions.
    • Comparative genomics capabilities are initiated by linking rice and Arabidopsis genomes.

    Conclusions:

    • OryGenesDB serves as a valuable resource for rice functional genomics research.
    • The database facilitates the study of gene function through insertion mutants.
    • OryGenesDB is a foundational step towards plant comparative genomics.