Fig. 3
Fine structure of centromere repeat arrays in three species of Brachypodium genus. a, b Histograms of CentBd or CentBs monomer length (bp) (a) and sequences identity (b) relative to the genome-wide consensus in Bd21-CEN (light red), Bst99-CEN (cyan), BhD (green), and BhS (purple) subgenome of IBd483-CEN assemblies. c The length of HOR unit in monomer pattern from Bd21-CEN (light red), Bst99-CEN (cyan), BhD (green), and BhS (purple) subgenome of IBd483-CEN assemblies. d CENH3 enrichment level [log2(ChIP/Input)] around CentBd or CentBs satellite, centromeric intact CRM (n = 142 in IBd483-CEN; n = 39 in Bd21-CEN; n = 35 in Bst99-CEN) and non-centromeric intact CRM (n = 138 in IBd483-CEN; n = 68 in Bd21-CEN; n = 49 in Bst99-CEN) elements in Bd21, Bst99, and IBd483 lines. e Circos plot showing CentBd or CentBs satellite density grouped by decreasing CENH3 log2(ChIP/Input) (light red, cyan, blue, green, yellow), and satellite density grouped by decreasing sequence identity (light red, cyan, blue, green, yellow) in each chromosome of the three genomes. Q scale means the satellite quantile grouped by CENH3 occupancy (top) or satellite sequence identity compared with consensus repeat (bottom). CENH3 enrichments (purple) across the centromeres of the three assembled genomes were shown in the innermost circos plot. f Dot plot of centromeric intact CRM elements from three genome assemblies using a 75-bp search window. Light red, cyan, and light green lines/boxes represent the centromeric regions from Bd21-CEN, Bst99-CEN, and IBd483-CEN genomes. Red and blue points indicate forward- and reverse-strand similarly, respectively. g Comparison of the insertion time of intact CRM elements from centromere (CEN_CRM) and non-centromeres (Non_CEN_CRM) between the D and S sub/genomes in Bd21-CEN, Bst99-CEN, and IBd483-CEN genomes. h Comparison of the sequence identities of satellite repeats near CRM insertions (CRM_insertion) and the interior regions of centromeres (Non_CRM_insertion) in all three assembles genomes. i A negative relationship between LTR density/100-kb (x axis) and satellite monomer identity (y-axis) in all the chromosomes from the three genomes. Light red, cyan, light green, and purple points represent the centromeric region from Bd21-CEN, Bst99-CEN, BhD, and BhS subgenome of IBd483-CEN genomes. Several large subblocks of satellite arrays in BhS4, BhS7, Chr05, Chr07, Chr08, and Chr1 were far apart and analyzed separately (as illustrated in Additional file 1: Fig. S18b-c). T-test, *P < 0.05, **P < 0.01, ***P < 0.001