Fig. 4
Genetic and epigenetic variation across centromeres from diploid to tetraploid in Brachypodium. a Comparison of the changes in centromere size and centromeric satellite copy number variations between homologous chromosome pairs from diploid to tetraploid in Brachypodium. Colored points represent the comparison between BhD-IBd483 and Bd21 (light red), as well as BhS-IBd483 and Bst99 (cyan). b Comparison of the proportion of satellite monomer duplications in the centromeres from homologous chromosome pairs between diploid to tetraploid in Brachypodium. Light red, cyan, light green, and purple points represent the sharing proportion of satellite repeats from Bd21-CEN, Bst99-CEN, BhD, and BhS subgenome of IBd483-CEN genomes. c, d CENH3 ChIP-seq mapping coverage from diploid lines Adi-3, Bd21 (c) or Bst92, Bst99 (d), and tetraploid IBd163, IBd483 lines to Bd21-CEN (c) or Bst99-CEN (d) genome with coordinates at top. The mapping coverage from IBd163, IBd483 and Adi-3, Bd21 (c) or Bst92, Bst99 lines (d) to IBd483-CEN genome with coordinates at left side. Forward- and reverse-strand satellite monomer sequences and top five ranked HOR arrays are annotated on CEN4 (c) and CEN07 (d) (Track 5–11). Dot plots compare the homologous centromeres between diploid to tetraploid Brachypodium using a search window of 156 bp. Red and blue points indicate forward- and reverse-strand similarity, respectively. e The structure and copy number of top five frequent HORs in the centromeres (CEN4 or CEN7) from homologous chromosomes between diploid to tetraploid Brachypodium. Light red, cyan, light green, and purple histograms represent the HOR structure from corresponding centromeres of Bd21-CEN, Bst99-CEN, BhD, and BhS subgenome of IBd483-CEN genomes. f PCA projection of 5-mer frequency vectors for centromeric satellite repeats (CentBd or CentBs) on PC1(first principal component) and PC2 (second principal component) from different assembled Brachypodium genomes. Each point represents an individual copy of satellite and colored according to the sub/genomes. Light red, cyan, light green, and purple points represent satellites from Bd21-CEN, Bst99-CEN, BhD, and BhS subgenome of IBd483-CEN genomes. Box plots on the top or right of PCA projection show the overall distribution of PC1 and PC2 scores between different sub/genome groups (T-test, ** P < 0.01). g, h Metaprofiles of CENH ChIP signals [log2(ChIP/Input)] around CentBd/CentBs satellite repeats (g) and centromeric intact CRM elements (h). The peaks reflect the distribution of CENH3 nucleosomes across the centromeric repetitive sequences. Different colored lines represent the CENH3 nucleosome distributions on CentBd/CRM repeat of Bd21 (light red, Bd21_CentBd/CRM), IBd483-BhD subgenome (light green, IBd483-BhD_CentBd/CRM), or on CentBs/CRM repeat of Bst99 (cyan, Bst99_CentBs/CRM), IBd483-BhS subgenome (purple, IBd483-BhS_CentBd/CRM)