Extended Data Figure 2. Classification and distribution of changes in SD content in the 65 genomes.

a) Schematic depicting the four categories of non-reference SDs: 1) new (i.e., unique in the reference), 2) expanded copy number, 3) content or composition changed, and 4) expanded and content changed SDs with respect to the SDs in the reference genome, T2T-CHM13. b) Quantification in terms of Mbp and predicted protein-coding genes across the four categories of new SDs compared to T2T-CHM13. The left panel shows the Mbp by category, while flagging those that are singleton (i.e., duplicated in T2T-CHM13 but not in other genomes). The right panel quantifies the number of complete (100% coverage) and partial overlaps (>50% coverage) with protein-coding genes for the respective chromosomes.