POGED: A Plant Orthologous Group Evolution Database

Comparative analyses of orthologous gene families are central to understanding the evolution of gene function and regulatory pathways across species. However, accurate and efficient orthology assignment across diverse plant and algal genomes remains challenging for many researchers with limited bioinformatics background. We designed a Plant Orthologous Group Evolution Database (POGED, http://poged.xhlab.ac.cn:30001/#/), which integrates orthology inference and domain annotation across 57 species. POGED includes the major evolutionary trajectory of land plants and algae, providing a comprehensive framework for robust evolutionary analyses. Specifically, POGED provides (i) an OrthoFinder-based Search module for orthogroup queries by protein identifiers with downloadable tables and phylogenetic trees; (ii) a PfamScan-based Search module for identifying proteins that share identical Pfam domain architectures and for querying by both protein and Pfam identifiers; (iii) a BLAST module for similarity searches against all integrated species; and (iv) a Submit module that enables users to upload custom protein datasets for orthogroup or domain architecture analyses. In addition, analysis of MAPK orthogroups and the protein kinase domain PF00069 (Pkinase) demonstrated that POGED is ideal for orthogroup-based phylogenetic analyses and cross-lineage comparisons of domain architectures. We also highlighted significant applications of POGED in gene family evolution analysis and gene discovery for function verification in plants.