De novo genes in plants: Origins, mechanisms, and functional implications

De novo genes originate from previously non-coding genomic regions and provide an important source of lineage-specific innovation. In plants, they may contribute to adaptation, trait diversity, and crop evolution. This review summarizes recent progress in research on plant de novo genes. We first discuss major routes of gene birth, including transcription-first, open reading frame-first, and concurrent models, and examine how nascent loci acquire regulatory control and enter existing biological networks. We summarize the evolutionary features of de novo genes, including weak early constraint, rapid molecular change, restricted expression, and structural refinement, and we provide examples of such genes involved in stress responses, seed germination, kernel dehydration, subspecies divergence, reproductive isolation, and floral scent diversification. Rapid sequence evolution, genome annotation quality, polyploidy, and transposable elements pose challenges to current methods for identification of de novo genes. We therefore discuss how whole-genome synteny alignment, multi-omics evidence, and machine-learning approaches can improve candidate discovery, while noting the important limitations of each method. Finally, we highlight key future questions related to functional validation, the latent coding potential of long non-coding RNAs, epigenetic activation, regulatory network integration, and crop improvement. These perspectives clarify how de novo genes have shaped plant adaptation and how they may be used in precision breeding and synthetic biology.