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Wanda: a database of duplicated fish genes.
Yves Van de Peer1, John S Taylor, Jayabalan Joseph
1Department of Biology, University of Konstanz, D-78457 Konstanz, Germany. yvdp@gengenp.rug.ac.be
Nucleic Acids Research
|December 26, 2001
Summary
Ray-finned fish possess numerous gene copies due to ancient and recent genome duplications. The Wanda database catalogs these gene families, aiding evolutionary and developmental studies.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Ray-finned fish (Actinopterygii) exhibit a higher gene copy number compared to other vertebrates.
- This expansion is attributed to a significant ancient genome duplication event predating the teleost radiation, alongside numerous lineage-specific duplications.
Purpose of the Study:
- To introduce Wanda, a curated database detailing orthologous gene groups across species.
- To provide resources for studying gene duplication and divergence in ray-finned fish.
Main Methods:
- Comparative genomics analysis to identify orthologous and paralogous gene relationships.
- Construction of sequence alignments and phylogenetic trees for relationship validation.
- Database curation including gene copy number, map positions, and functional data.
Main Results:
- Wanda database successfully lists orthologous gene groups with representatives from human, mouse, chicken, Xenopus, and ray-finned fish.
- Includes sequence alignments and phylogenetic trees to support orthology and paralogy assignments.
- Incorporates available map positions and functional annotations for genes.
Conclusions:
- The Wanda database serves as a valuable resource for researchers investigating gene evolution and functional divergence post-duplication.
- Facilitates comparative genomic studies within Actinopterygii and across vertebrates.