Extended Data Fig. 6: The comparative analysis on macaque centromeres.

(a) The dot plot shows the chr. 1 α-satellite arrays between MFA and MMU, generated with UniAligner. The red dots refer to the common rare k-mers (k ≥ 80) and the green dots refer to the conserved regions between two centromeres. The black line indicates the optimal rare alignment path. The α-satellite array strand track is shown above the dot plot (blue for forward strand (+) and red for reverse strand (–)). (b) The SF and methylation patterns of α-satellite arrays on chr. 1 for both MFA and MMU are depicted. Sequence similarity within the 5 kb block is visualized using ModDotPlot, with the CDRs highlighted in red by corresponding methylation levels. (c) The green, red, and blue violin plots represent the length distribution of α-satellite arrays for HSA, MFA, and MMU, respectively. The horizontal lines indicate the length of reference genomes (green for T2T-CHM13v2.0 and red for T2T-MFA8v1.1). Box plots show median and IQR, with whiskers 1.5×IQR. The P values are calculated with the two-sided Mann-Whitney U test, and the number of assembled centromeres is indicated in parentheses below each plot. NS: not significant. (d) The phylogenetic tree shows that the S1 (red), S2a (blue), S2b (green), and SF9 α-satellites (dark gray) of MFA (round) and MMU (triangle) mixed in their respective separate clades. (e) The phylogeny trees for monomers of S1S2 dimers from MFA chr. 8 (yellow), chr. 11 (red) and chr. 17 (lilac). S2a has chromosome-specific variants while S1 and S2b do not.