Unravelling the processes controlling pollen formation and functions with cross-species comparative analysis

Abstract Pollen and anthers are essential for plant reproduction, yet the genetic mechanisms governing their formation and function remain incompletely understood. In this study, we performed a comprehensive cross-species comparative analysis leveraging 16,904 RNA-seq samples from 90 plant species, encompassing diverse lineages from bryophytes to angiosperms. By calculating tissue specificity metrics and applying clustering and functional enrichment analyses, we identified both conserved and lineage-specific gene families associated with pollen and anther development. Our computational pipeline allowed for the discovery of previously unstudied genes and predictions of their critical biological roles, which were experimentally validated through mutant characterization, genotyping, and detailed morphological analysis. Notably, we observed evolutionary patterns in pollen morphology, cell wall structure, cytoplasmic content, and aperture characteristics, highlighting differences and gradual transitions among major plant clades. These findings provide significant insights into the evolutionary processes shaping pollen and anther traits, and establish a valuable resource for future studies in plant reproductive biology and biotechnology.