The role of chromosome segmental mutations in eukaryotic pangenome evolution

Emerging pangenome studies have revealed that genomic content is not universally shared among all individuals of a species, in both prokaryotes and eukaryotes. While frequent horizontal transfer is thought to be the main driver of presence/absence variation (PAV) in prokaryotic pangenomes, the mechanisms that generate PAV in eukaryotic species remain poorly understood. Here we investigate the contribution of large-scale chromosomal structural variants, segmental mutations (SMs) – long duplications and deletions, to pangenome variation. Using mutation accumulation lines of a representative species with a highly variable pangenome, the coccolithophore Gephyrocapsa huxleyi , we estimate the rate of SMs for a diploid strain to be 1.22×10−2 per haploid genome per generation, approximately seven- to eightfold less frequent than the single-nucleotide mutation rate, with SM sizes ranging from 0.03 to 10.14 Mb (mean ~1.55 Mb). SM breakpoints are enriched in repeat-rich regions, consistent with contributions from both DNA transposon-associated DNA breakage and error-prone DNA double-strand break repair pathways. Extending our analyses across additional planktonic and model species with characterized pangenomes indicates that SMs represent a widespread and dynamic source of genome variation. This supports the role of segmental duplications and deletions as an important source of PAV variation and accessory genomic content in eukaryotic pangenomes. The recurrent formation of SMs, together with their subsequent fixation or loss, generate accessory genes and remodel pangenome structure, providing a mechanistic basis to eukaryotic pangenome evolution.