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FUNYBASE: a FUNgal phYlogenomic dataBASE.

Sylvain Marthey1, Gabriela Aguileta, François Rodolphe

  • 1UR MIG, INRA, Bâtiment 233 Domaine de Vilvert 78350, Cedex, France. sylvain.marthey@jouy.inra.fr

BMC Bioinformatics
|October 29, 2008
PubMed
Summary
This summary is machine-generated.

FUNYBASE provides fungal orthologous gene families for evolutionary studies. This database aids comparative genomics and improves phylogenetic reconstruction by identifying informative genes.

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Area of Science:

  • Fungal genomics
  • Bioinformatics
  • Evolutionary biology

Background:

  • Increasing fungal genome sequences offer protein data for evolutionary and phylogenetic analyses.
  • Data heterogeneity and annotation quality pose challenges for fungal evolutionary studies.
  • A reliable resource for orthologous gene families is needed for fungal comparative and phylogenetic analyses.

Purpose of the Study:

  • To establish FUNYBASE, a database of fungal orthologous gene families.
  • To classify fungal genes into reliable ortholog clusters.
  • To assess the phylogenetic informativeness of fungal orthologs.

Main Methods:

  • FUNYBASE analyzes fungal single-copy genes from public genome sequences.
  • Ortholog clusters are identified using a robust automated procedure.
  • Phylogenetic trees are reconstructed from amino acid sequences and compared to a reference species tree using a topological score.

Main Results:

  • The database includes protein sequences from 30 fungal genomes classified into ortholog clusters.
  • A subset of 246 ortholog clusters, present as single-copy genes in 21 genomes, was analyzed.
  • Orthologs were scored based on their ability to recover the reference species tree topology.

Conclusions:

  • FUNYBASE offers a novel resource for comparative genomic studies using orthologous gene clusters.
  • The database enhances phylogenetic reconstruction by identifying genes with high informative value.
  • User-friendly online access facilitates searches by species, gene cluster, keywords, or BLAST.