Fig. 2

Comprehensive map of centromeres in Brachypodium genus. a, b Characteristics of the centromeres in Brachypodium genome assemblies. CENH3 enrichment [log₂(ChIP/Input)] plotted over centromere BhD4 (ChIP samples from IBd163 and IBd483) in IBd483-CEN and CEN4 (ChIP samples from Adi-3 and Bd21) in Bd21-CEN assembled genome (a), and centromere BhS2 in IBd483-CEN and CEN02 (ChIP samples from Bst92 and Bst99) in Bst99-CEN assembled genome (b). Different layers demonstrate the CENH3 enrichment, CentBd or CentBs distribution with forward- (red) or reverse- (green) strand orientations, the structure of top five ranked frequent HORs (higher-order repeats), TE (transposon element) annotations, and heatmap of pairwise CentBd or CentBs satellite sequence similarity, respectively. c Dot plots comparing the centromeres from distinct genome assemblies using a search window of 300 bp. 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 similarity, respectively. d Phylogenetic tree of all CentBd (red) and CentBs (blue) repeats with branches colored by subgenomes in IBd483-CEN (top), or by Bd21-CEN and Bst99-CEN genomes (bottom). e Oligo-FISH mapping of satellite repeats on metaphase chromosomes of IBd483, IBd163, Bd21, and Bst99 lines. Oligo-probes (probes 1a + 2a for CentBd (red) and probes 1b + 2b for CentBs (green), as illustrated in Additional file 1: Fig. S11b) are hybridized simultaneously. The boxed insets show higher-magnification views of chromosomes. Chromosomes are colored in blue with 4’,6-diamidino-2-phenylindole (DAPI). Scale Bar = 10 μm. f Phylogenetic tree of all CRM retrotransposons within the core centromeres. The branches are colored by subgenomes in IBd483-CEN (red for BhD subgenome and blue for BhS subgenome, top), or by Bd21-CEN (red) and Bst99-CEN (blue) genome (bottom)