GreenPhylDB v5: a comparative pangenomic database for plant genomes

Area of Science:

• Plant genomics
• Bioinformatics
• Evolutionary biology

Background:

• Comparative genomics is crucial for understanding evolutionary and functional genomic relationships.
• Existing databases often rely on single reference genomes, limiting comprehensive orthology detection.
• The increasing number of sequenced plant genomes necessitates advanced comparative approaches.

Purpose of the Study:

• To introduce GreenPhylDBv5, a database enabling comparative pangenomics by utilizing multiple genome sequences per species.
• To enhance the exploration of gene families and homologous relationships in plant genomes.
• To provide updated tools and a platform for community-driven curation.

Main Methods:

• Harnessing multiple genome sequences per species for comparative pangenomics.
• Building gene families and predicting homologous relationships using phylogenetic-based analyses.
• Incorporating new tools for protein-domain combinations, tree topology searches, and user data storage.

Main Results:

• GreenPhylDBv5 was developed, considering 46 plant species and creating 19 pangenes.
• The database facilitates the analysis of gene families and homologous relationships across diverse plant genomes.
• An updated website with novel tools and community curation features was launched.

Conclusions:

• GreenPhylDBv5 advances comparative genomics by enabling pangenomic analyses across multiple plant genomes.
• The database provides a valuable resource for evolutionary and functional genomic research, particularly for staple crops.
• Enhanced tools and community features improve usability and foster collaborative research efforts.