Fig. 3: Characterization of the structure of putative centromeric repeats in gayal chromosome 1 (BFR1) derived from Rob (2,28).

a Schematic illustration of centromeric fusion model for Rob (2,28) in Bos frontalis. BTA2 and BTA28 represent chromosomes 2 and 28 on Bos taurus, respectively. BFR1 indicates chromosome 1 on Bos frontalis. Scaffold60 is an abbreviation for Fragscaffold60, which is identified as a putative centromere-fusion scaffold in BFR1. The circle indicates the centromere region and the triangle indicates the satellite repeat. Considering the continuity of gene positions, we divide 17 syntenic genes, represented by black lines, into 7 alignment segments, where 5 segments with 9 genes in BTA2 and 2 segments with 8 genes in BTA28. b Phylogenetic analysis of the centromeric satellite I repeats in BTA2 (green), BTA28 (blue), and Scaffold60 (pink). c The mode of satellite repeat organization in centromere core characterized as the higher-order arrays. Based on high sequence identity in repeat monomer alignments, consecutive ordering and orientation, two blocks on BTA2, eight blocks on BTA28, and three blocks on Scaffold60 are identified in the centromere regions, respectively. Each block is composed of a multimeric satellite array representing a semitransparent arrow, called higher-order repeats (HORs) in humans and primates, in which the constituent monomers are distinguished (greater than 85% sequence identity). Solid arrows represent monomeric repeat units, with green and purple arrows depicting direct and inverted orientation respectively. Random insertions (purple rectangle) are found interspersed among the blocks. The illustrated syntenic patterns (gray parallelogram shading) describe the correspondences of the three satellite blocks in Scaffold60 with blocks in BTA2 and BTA28, respectively, having the highest homology in the alignment of the consensus sequences between blocks. d CENP-B box-like motifs extracted from consensus satellite sequences. The alignment of the CENP-B box sequences and its flanking regions are shown (Supplementary Fig. 7). Two motifs are comparable to the consensus CENP-B box respectively, where nine core nucleotides are denoted in red and the identical motif is “YTCCAGWYRARGCAGGR.” e Nucleotide substitution of full-length satellite repeat consensus sequences. Transitions (Ts, 34/105) are represented in blue, and transversions (Tv, 71/105) are represented in pink. Dashes indicate identical bases and dots indicate deletion. Red rectangle shows the location of CENP-B box in satellites.