Fig. 4
From: Four near-complete genome assemblies reveal the landscape and evolution of centromeres in Salicaceae
Characteristics of non-centromeric Palv148 TRAs. a Characteristics and epigenetics for Palv148 TRAs in chr09 of P. alba var. pyramidalis haplotype II. Plots from top to bottom separately represent TRAs on forward (red) and reverse (blue) strands and CENH3 CUT&Tag distribution per 10-kb, transposable element distribution per 10-kb, DNA methylation level per 10-kb, histone modification level per 10-kb, gene distribution, CRM element distribution and sequence similarity on centromeres and adjacent regions. b and c show histograms of Palv148 monomer lengths (left) and variant distances relative to the genomewide consensus (right) in P. alba var. pyramidalis haplotype I and haplotype II, respectively. d Phylogenetic tree of sampled Palv148 and Sar145 monomers. The color of the outer circle and the tree branch represented the corresponding chromosome and genome haplotype, respectively. e Boxplot of Palv148 and Sar145 TRAs monomer similarity comparisons in both within and between chromosomes, haplotypes, and species. f and g show histograms of monomer number (length) of Palv148 in HOR blocks (left) and the distances between HORs (right) in P. alba var. pyramidalis haplotype I and haplotype II, respectively. h Representative Palv148 TRA region heatmap colored according to pairwise variants between Palv148 monomers. i Hi-C interaction strengths comparisons of Palv148 TRAs with centromeres and non-centromeric regions, respectively (two-tailed Wilcoxon rank-sum test, ****P ≤ 0.0001, ***P ≤ 0.001, **P ≤ 0.01, *P ≤ 0.05, ns: not significant)