Fig. 2: Genome structure of centromeric regions in the C. annuum genome.

a Schematic representation showing the distribution of different transposable elements across 12 centromeres in CaT2T. The CENH3 ChIP-seq signals (average of two biological replicates) are represented by the enrichment level in 30 kb windows and the ChIP-identified centromeres are marked by gray boxes. The red lines for the track of the CRM indicate that the intact CRM was located in the centromeres. b Specific LTR insertion time distribution of the whole genomes and centromeres. The central white line and black line in the plot indicate the median and the upper and lower quartiles of insertion times respectively. Significant differences between groups were assessed using the two-sided Wilcoxon rank-sum test. c Specific ratio of solo LTR to intact LTR-RT distributions in the whole genomes and centromeres. Significant differences between groups were assessed using the two-sided Wilcoxon rank-sum test. d Neighbor-joining trees constructed from genome-wide intact Ty3-Gypsy elements from C. annuum, C. rhomboideum and S. tuberosum. The red, green and yellow solid circles in the branches represent the elements located in centromeric regions. e An example of pairwise sequence identity of nonoverlapping 5 kb centromeric regions in C. annuum and C. rhomboideum. Source data are provided as a Source Data file.