PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference

Area of Science:

• Plant genomics
• Evolutionary biology
• Bioinformatics

Background:

• Gene function knowledge transfer across plant species is hindered by gene and genome duplications.
• Complex evolutionary histories, including orthologs and paralogs, complicate functional inference based solely on sequence similarity.

Purpose of the Study:

• To develop an accessible online resource for accurate and efficient gene function knowledge transfer in plants.
• To facilitate functional inference for uncharacterized plant genes by leveraging evolutionary relationships.

Main Methods:

• Development of the PhyloGenes online resource (phylogenes.org).
• Precomputation of phylogenetic trees for plant gene families.
• Integration of experimentally validated gene function data (e.g., Gene Ontology terms) with phylogenetic trees.
• Labeling of evolutionary events (speciation, duplication) on gene trees.

Main Results:

• PhyloGenes represents 40 plant genomes and 10 non-plant model organisms across over 8,000 gene families.
• Nearly 6,000 families include genes with experimentally supported Gene Ontology annotations.
• The resource visually displays gene function data within evolutionary contexts, distinguishing orthologs from paralogs.

Conclusions:

• PhyloGenes enables visually traceable functional inference for uncharacterized genes based on evolutionary history.
• The resource aids in understanding divergent gene functions arising from evolutionary events.
• Future enhancements include integrating plant gene expression atlas data.