From structural pangenomes to functional panomics in plants.

Understanding how genome structure and gene content evolve within and among plant species requires analytical frameworks that capture the full spectrum of allelic and structural variation. Plant pangenomes have progressed from gene-focused and linear representations to chromosome-scale, haplotype-resolved graphs that preserve allelic and structural diversity across populations. Attention is increasingly focused on the evolutionary processes that generate and maintain pangenome architecture, alongside the adoption of graph-based coordinate systems that reduce reference bias and enable multi-omics integration. Here, we review plant pangenome paradigms, from early homology-based gene sets to haplotype-resolved graph models, and summarize tradeoffs in construction, mapping, and variant analysis. We synthesize patterns of core and variable gene compartments across studies and examine how transposable elements, gene duplication, and selection shape their contrasting evolutionary dynamics. Using panNLRomes and crop domestication as case studies, we illustrate how graph-based frameworks clarify evolutionary and functional signals obscured by single references, including birth-death dynamics at resistance loci and structural variants associated with domestication. Finally, we discuss emerging applications in pantranscriptomics and panepigenomics and outline key methodological and infrastructural challenges.