Pangenomes provide new insights into polyploidy in plants

Abstract Polyploidy, also known as whole-genome duplication (WGD), is a significant evolutionary force in green plants, especially angiosperms. The dynamic nature of polyploid genomes generates genetic diversity and drives the evolution of novel traits and adaptations. Pangenomics is emerging as a major frontier in plant genome research, with a rapidly growing number of pangenomes for individual species and associated analyses providing novel agronomic and evolutionary insights. Polyploid genome analysis can be confounded by intraspecific variation when relying on a single reference genome assembly. The use of pangenomes that better represent the genomic diversity of a species helps overcome this limitation. ­However, a major gap remains between the number of pangenomic studies in polyploid compared to diploid species, despite the widespread prevalence of WGD, limiting the potential of the pangenome framework for characterizing and understanding polyploid genomes. Furthermore, most polyploid pangenome studies have focused on domesticated crop species, and natural populations have rarely been examined. In addition to applications in crop improvement, pangenomes can provide insights into the ecological and evolutionary impact of polyploidy. Here, we summarize recent pangenome studies in polyploid plants and highlight promising topics for future research. We hope this article will encourage the growth of pangenomic studies in polyploid systems, particularly in natural populations.