Abstract: Unlike most plants with localized monocentromeres, some Magnoliales species possess holocentric chromosomes. To investigate the genomic basis of this difference, we generated chromosome-level genomes for the holocentric species Myristica fragrans and the monocentric species Cananga odorata and performed comparative multi-omics analyses. We found that C. odorata shows localized heterochromatin enrichment and clustered transposable elements, whereas M. fragrans exhibits a more dispersed chromatin organization. Despite these differences, centromere-associated regions in both species are positively associated with mCG/mCHG and heterochromatin-related chromatin compartments, while differing in mCHH patterns and repetitive sequence landscapes. Our analyses further suggest that the emergence of holocentricity in Myristica is unlikely to be explained by whole-genome duplication events or major structural changes in core kinetochore proteins. Instead, lineage-specific remodeling of repetitive sequences and epigenetic states may have contributed to centromere reorganization. These results provide new insights into centromere diversification in Magnoliales.

Key words: centromere evolution, comparative genomics, genome, holocentromere, transposable elements