Fig. 5.

An overview of centromere identification based on Hi-C data. a A diagram of Hi-C data mapping against the reference genome. b Characterization of centromeres in Hi-C heat maps. The left panel shows chromatin interactions, including G. davidsonii mapped to G. thurberi (D₃_map_D₁) and G. thurberi mapped to G. thurberi (D₁_map_D₁). The middle panel presents a genomic alignment around the centromeres. The three-dimensional rings indicate the centromeres. The right panel shows chromatin interactions, including G. davidsonii mapped to G. davidsonii (D₃_map_D₃) and G. thurberi mapped to G. davidsonii (D₁_map_D₃). The regions within the orange lines are the centromere regions. c Validation the centromeres by centromeric LTR (Centromere Retroelement Gossypium, CRG) BLAST analysis. The data showed the validation on Chr08. d Centromere feature analysis. The right panel presents a comparison of the repetitive elements for centromeres vs. the whole genome. The middle shows LTR insertion time distributions for centromeres specifically, and for the whole genome. The center red line in the plot indicates the median, and the black lines indicate the upper and lower quartiles for insertion times. The right panel shows an analysis of the intact LTR insertion pattern. An example is presented for G. thurberi Chr04. The digits present the insertion time of nearby LTRs. e Analysis of centromere LTR enrichment. The left panel represents the sequence identity characteristic of a “CentLTR” sequence, as examined in centromeres and non- non-centromeric regions in four D genomes. The right panel is the identity distribution pattern of CenLTR hits presented as a dot plot. This analysis detected a total of 152,285 CenLTRs in D₁ centromeres, with 163,217 in D₁ non-centromeric regions; 158,815 in D₃ centromeres, with 139,231 in D₃ non-centromeric regions; 16,093 in D₅ centromeres, with 76,875 in D₅ non-centromeric regions; and 80,537 in Gh_D_t1 centromeres, with 246,791 in Gh_D_t1 non-centromeric regions