MaizeGDB phylostrata tool: exploring evolutionary origins of maize proteins

Authors: TIBBS-CORTES, LAURA - Oak Ridge Institute For Science And Education (ORISE); HALEY, OLIVIA - Oak Ridge Institute For Science And Education (ORISE); Portwood Ii, John; Cannon, Ethalinda; Woodhouse, Margaret; Andorf, Carson

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/27/2026
Publication Date: N/A
Citation: N/A

Interpretive Summary: Corn breeders and researchers need simple ways to identify which genes are widely shared across plant and animal kingdoms versus newer and corn-specific, because a gene’s evolutionary history can help prioritize stable, essential targets for improving yield, tolerance, and disease resilience. This information has been difficult to access consistently across major U.S. corn lines. To address this, we developed the MaizeGDB Phylostrata Tool, a public web application with interactive visualizations and summary tables for each of corn’s forty thousand proteins showing the evolutionary origin alongside descriptions of each gene's function. The resource provides data downloads for 26 maize inbred varieties. We also released an updated, open-source codebase that is more robust to data updates, along with example scripts that can help other species/crop communities run similar analyses and build comparable tools. By making evolutionary origin and conservation information easy to explore and download at scale, this resource speeds gene prioritization and reduces redundant analysis, helping accelerate the development of improved maize varieties that strengthen the reliability of the U.S. corn supply and deliver practical benefits to American farmers and the public through more resilient crops, reduced production risk, and greater long-term food and agricultural stability.

Technical Abstract: Motivation: Phylostratigraphic analysis identifies the evolutionary origins and level of conservation of proteins, with applications in evolutionary biology and comparative genomics. Results: We developed the MaizeGDB Phylostrata Tool, a custom web application that enables users to explore the evolutionary origins of maize proteins. This tool features interactive visualizations and detailed gene pages incorporating subcellular localization, Gene Ontology terms, and other resources for homologs. Full-proteome downloads are available for 26 maize inbreds (B73 and the NAM founders). We also provide an updated version of the 'phylostratr' R package that makes it more robust to taxonomic updates, as well as example scripts for phylostratigraphic analysis and webtool development for the use of researchers and curators of other species.