Comparative centromere genomics reveals evolutionary divergence in Solanaceae genomes

Centromeres are chromosomal loci epigenetically specified by the histone variant CENH3, where kinetochores assemble to ensure accurate chromosome segregation during cell division. Their repetitive and rapidly evolving DNA has long impeded large-scale characterization. Advances in long-read sequencing now enable complete genome assemblies across species and within populations, providing opportunities to investigate how centromeres evolve and diversify over timescales from thousands to millions of years.

Here, we generate near-telomere-to-telomere genome assemblies for eggplant, African eggplant, and wild pepper. Using CENH3 ChIP-seq, we delineate functional centromeric chromatin in these assemblies and in the cultivated pepper 'CA59', tomato 'Heinz 1706', and a wild tomato accession. These genomes harbor satellite-free centromeres across all chromosomes except chromosome 3 in tomato and its wild progenitor. Instead, centromeres are primarily composed of Ty3/Gypsy LTR retrotransposons, whose clade composition, abundance, recent activity, and spatial distribution differ among species. Centromere size scales with genome size in Solanaceae crops. Comparisons of closely related genomes reveal frequent centromere positional shifts driven by pericentromeric inversions and centromere repositioning. Synteny decays more rapidly around centromeres, consistent with elevated breakage within CENH3-binding regions. Finally, centromere haplotypes vary within species, exemplified by multiple haplotypes on four African eggplant chromosomes.

These findings highlight the remarkable evolutionary dynamics and within-species variation of centromeres in Solanaceae crops, revealing distinct species-specific organizational patterns. This study positions Solanaceae as a promising model for comparative analyses of plant centromere evolution and provides a foundation for future research exploring how centromere variation contributes to phenotypic diversity.