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PineappleDB: an online pineapple bioinformatics resource.

Richard L Moyle1, Mark L Crowe, Jonni Ripi-Koia

  • 1Department of Botany, University of Queensland, QLD 4072, Brisbane, Australia. r.moyle1@mailbox.uq.edu.au

BMC Plant Biology
|October 6, 2005
PubMed
Summary

PineappleDB offers a new bioinformatics resource for pineapple genetics, detailing expressed sequence tags from fruit and roots. This database aids research into fruit ripening and nematode interactions.

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Area of Science:

  • Plant Science
  • Bioinformatics
  • Genetics

Background:

  • Limited understanding of non-climacteric fruit ripening mechanisms.
  • The molecular basis of nematode-plant interactions in pineapple roots is largely unknown.
  • A novel expressed sequence tag (EST) sequencing program was initiated to address these knowledge gaps.

Purpose of the Study:

  • To develop a comprehensive bioinformatics resource for pineapple research.
  • To provide access to curated EST data from pineapple fruit, root, and nematode-infected gall tissues.
  • To facilitate investigation into pineapple genetics, fruit ripening, and plant-nematode interactions.

Main Methods:

  • Creation of PineappleDB, an online, curated database.
  • Integration of annotated EST data, including splice variants and functional classifications.

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  • Implementation of text and BLAST search functionalities for sequence homology.

    • Main Results:

    • The database contains over 5600 EST sequences and 3383 contig consensus sequences.
    • Associated bioinformatic data includes Arabidopsis homologues and Gene Ontology classifications.
    • User-friendly search tools provide comprehensive sequence and functional information.

    Conclusions:

    • PineappleDB offers a valuable, accessible resource for the research community.
    • Efficient data mining is enabled through integrated search tools.
    • The database supports research in pineapple genetics, fruit ripening, nematode infection, and plant RNA splicing.