Portwood, J. | bioRxiv Science

bioRxiv2025

MaizeGDB Phylostrata Tool: Exploring evolutionary origins of maize proteins

MotivationPhylostratigraphic analysis identifies the evolutionary origins and level of conservation of proteins, facilitating research in evolutionary biology and comparative genomics. ResultsWe 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 ImplementationThe 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. Contactcarson.andorf@usda.gov

bioinformatics↗

bioRxiv2025

Extensive genome evolution distinguishes maize within a stable tribe of grasses

Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy - a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives Zea and Tripsacum. In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus Zea, 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.

evolutionary biology↗