FUNYBASE: A Database for Fungal Phylogenomic Analysis
Author Information
Author(s): Marthey Sylvain, Aguileta Gabriela, Rodolphe François, Gendrault Annie, Giraud Tatiana, Fournier Elisabeth, Lopez-Villavicencio Manuela, Gautier Angélique, Lebrun Marc-Henri, Chiapello Hélène
Primary Institution: INRA
Hypothesis
The study aims to provide a reliable and integrated resource of orthologous gene families for comparative and phylogenetic analyses in fungi.
Conclusion
FUNYBASE is a valuable resource for comparative studies and phylogenetic reconstruction in fungi.
Supporting Evidence
- FUNYBASE contains a complete set of protein sequences extracted from 30 public fungal genomes.
- The database includes 246 reliable ortholog clusters present as single copy genes in 21 fungal genomes.
- Phylogenetic trees were reconstructed based on amino acid sequences of the ortholog clusters.
- Each ortholog cluster was assessed for its informative value for phylogenetic reconstruction.
Takeaway
FUNYBASE is like a big library that helps scientists study how different fungi are related by looking at their genes.
Methodology
The study used a robust approach based on BLAST comparisons and Markov Cluster Algorithm classification to determine reliable clusters of single-copy orthologous genes in fungi.
Potential Biases
Potential biases include the accuracy of gene prediction and the clustering algorithm used.
Limitations
The study may be limited by the quality of genome annotations and the presence of multi-domain proteins that can generate artificial clusters.
Digital Object Identifier (DOI)
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