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The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics.

Christian Roth1, Matthew J Betts, Pär Steffansson

  • 1Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway.

Nucleic Acids Research
|December 21, 2004
PubMed
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This study analyzed gene families in plants and animals, identifying branches with high substitution rates as candidates for functional adaptation. The findings are compiled in The Adaptive Evolution Database (TAED) for evolutionary research.

Area of Science:

  • Evolutionary biology
  • Genomics
  • Bioinformatics

Background:

  • Gene families are fundamental units of genomic evolution.
  • Understanding gene family evolution provides insights into functional adaptation.
  • Comparative genomics requires robust databases for analyzing evolutionary patterns.

Purpose of the Study:

  • To generate and analyze large-scale gene families from embryophytes (higher plants) and chordates.
  • To identify gene family branches exhibiting signs of functional adaptation.
  • To create a publicly accessible database of evolutionary genomic information.

Main Methods:

  • Generated 4216 embryophyte and 15,452 chordate gene families from extensive gene datasets.
  • Performed multiple sequence alignments and constructed phylogenetic trees.

Related Experiment Videos

  • Calculated non-synonymous to synonymous substitution rate ratios (Ka/Ks) and mapped gene trees to NCBI taxonomy.
  • Linked gene family data to Protein Data Bank (PDB) structures.

    • Main Results:

    • Identified 173 embryophyte and 505 chordate gene family branches with Ka/Ks >> 1, indicating potential functional adaptation.
    • Compiled comprehensive data including alignments, trees, substitution rates, and structural information.
    • Developed 'The Adaptive Evolution Database' (TAED) for phylogenetic and evolutionary analysis.

    Conclusions:

    • The study provides a valuable resource for investigating adaptive evolution in plants and animals.
    • The identified candidate branches offer targets for further research into functional adaptation mechanisms.
    • TAED serves as a crucial platform for comparative genomics and evolutionary studies.