Dynamics of genome evolution in the era of pangenome analysis

The advent of long-read sequencing and telomere-to-telomere (T2T) assemblies has transformed studies of eukaryotic genomic variation. Pangenomes now leverage these advances to generate comprehensive catalogs of structural variants (SVs) and gene presence-absence polymorphisms across populations. Here, we review how pangenomes improve the identification, classification, and large-scale analysis of SVs and gene families, yielding insights into genome organization, functional gene evolution, and the architecture of phenotypic traits. We discuss mechanisms of SV formation, their uneven genomic distribution, and their roles in trait diversity. Examples from humans, plants, animals, and fungi highlight the importance of SVs in adaptation, domestication, and disease. We also consider the integration of pangenome graphs into genome-wide association studies, the challenges of applying T2T pangenomes at the population scale, and the need for new computational tools. Together, pangenomes represent a transformative framework for decoding genomic diversity and its consequences.