Computational tool development reveals evolutionary ages and conservation patterns of proteins across 26 maize lines, highlighting resources for comparative plant genomics.
Motivation Phylostratigraphic analysis identifies the evolutionary origins and level of conservation of proteins, facilitating research 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 (GO) 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. Availability and Implementation The MaizeGDB Phylostrata Tool is freely available at phylostrata.maizegdb.org . Scripts used for the analysis and web tool are available at https://github.com/LTibbs/PhylostrataWebtool . Contact carson.andorf@usda.gov
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