PLAZA dicots

PLAZA dicots provides comparative genomics resources for dicotyledonous plants by integrating genomic sequences, gene families, protein domains, phylogenetic trees, and functional annotations from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB, and PlantTFDB to support analysis of genome organization and gene function.

Key Features:

• Expanded Genomic Data: Database coverage increased to include 37 diverse dicot species, representing over four times the number of genomes since the initial release.
• Phylogenetic Range: Broader phylogenetic sampling with more detailed representation within specific clades, including additional crop species.
• Comprehensive Functional Annotation: Functional annotations enriched with Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB, and PlantTFDB data sources.
• Annotation Transfer Algorithms: Algorithms are used to transfer functional annotations from well-characterized plant genomes to other species.
• Gene Families and Phylogenetics: Inclusion of gene family classifications, protein domain annotations, and phylogenetic trees for comparative analyses.

Scientific Applications:

• Comparative Genomics: Comparative analysis of genome organization across model and non-model dicot species.
• Functional Annotation Propagation: Propagation of functional annotations from characterized genomes to less-annotated species to aid functional inference.
• Gene Family and Phylogenetic Studies: Investigation of gene family composition and evolutionary relationships using protein domains and phylogenetic trees.

Methodology:

Integrates genomic data from 37 dicot species; enriches annotations with Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB, and PlantTFDB; applies algorithms to transfer functional annotations from well-characterized genomes; and constructs gene families, protein domain annotations, and phylogenetic trees.