GreenPhylDB

GreenPhylDB provides comparative and functional genomics resources across the Plantae kingdom by organizing complete genomes from algae to angiosperms into gene families and inferring phylogenomic and orthologous relationships.

Key Features:

• Genome Repository: Version 2 includes sixteen full genomes that are automatically clustered into gene families for comparative analyses.
• Manual Annotation and Phylogenetic Analysis: Each gene family undergoes manual annotation followed by phylogenetic analysis to elucidate orthologous and paralogous relationships.
• Comprehensive Gene Family Lists: Provides plant-specific, phylum-specific, and species-specific gene family lists.
• Gene Family Ontology Browser: Offers an analysis tool to explore gene family ontology mappings.
• Integration with External Databases: Integrates annotations and cross-references from UniProt, KEGG, InterPro, TAIR, and TIGR.
• Phylogenomic Relationships: Contains 6,421 manually curated plant gene families with phylogenomic relationships computed for 4,375 families, including TAIR, InterPro, and KEGG families and subfamilies curated using TribeMCL.
• Orthologous Group Creation: Employs a semi-automatic clustering procedure to assign sequences from Oryza sativa and Arabidopsis thaliana to gene families and creates orthologous groups via a phylogenomic approach.
• GreenPhyl Ortholog Search Tool (GOST): Predicts orthologous relationships between O. sativa/A. thaliana proteins and sequences from other plant species.

Scientific Applications:

• Comparative Genomics: Enables cross-species comparisons across a broad taxonomic range from algae to angiosperms.
• Phylogenomics and Evolutionary Analysis: Supports inference of phylogenomic relationships and the study of orthology and paralogy to investigate evolutionary dynamics.
• Gene Discovery and Functional Annotation: Facilitates gene discovery and transfer of functional annotations through orthology and integrated database evidence.
• Taxon-specific Investigations: Allows identification and analysis of plant-specific, phylum-specific, and species-specific gene families for studies of plant genetics, evolution, and biodiversity.

Methodology:

Data processing includes automatic clustering of genomes into gene families with curation using TribeMCL, manual annotation and phylogenetic analysis to infer orthologs and paralogs, a semi-automatic clustering procedure for assigning Oryza sativa and Arabidopsis thaliana sequences, creation of orthologous groups via a phylogenomic approach, integration of annotations from UniProt, KEGG, InterPro, TAIR and TIGR, and ortholog prediction using the GreenPhyl Ortholog Search Tool (GOST).