Fig. 2: Dynamics of einkorn centromeres.

a, The composition of the TA299 chromosome 3A centromere. The top track shows CENH3 ChIP–seq coverage. The vertical lines underneath the track indicate genes. The bottom track shows TE composition. The x axis indicates chromosomal positions in megabases. The functional centromere is highlighted (blue shading). b, Dot plot alignment of chromosome 4A centromeric regions of TA299 (horizontal) and TA10622 (vertical). CENH3 ChIP–seq coverage and positions of RLG_Cereba insertions are aligned with the dot plot. RLG_Cereba insertion age is colour-coded in million of years (Myr). Rearranged chromosomal segments are shown in colours that correspond to those in c. The small rectangle indicates an approximately 400 kb region that is shown in detail in d. c, Evolutionary model explaining the organization of chromosome 4A centromeres in TA10622 and TA299. A–E indicate segments that experienced inversions compared with the ancestral centromere. X–Z represent segments that were deleted in one of the two accessions. d, Comparison of the shifted TA299 chromosome 4A centromere with its counterpart in TA10622. Conserved sequences are connected by the shaded grey areas. New TE insertions are shown partially raised. All new TE insertions are of the RLG_Cereba and RLG_Quinta families. e, Evidence of an additional inversion of around 10 Mb in chromosome 1A that moved part of the functional centromere (indicated by the two-headed arrow). Top, CENH3 ChIP–seq coverage. Bottom, the chromosomal positions of RLG_Cereba and RLG_Quinta retrotransposons (x axis) and their insertion age (y axis). The distribution and insertion ages of retrotransposons indicate that the inversion occurred around 500,000 years ago (grey dashed line) in a common ancestor of TA10622 and TA299. f,g, Examples of how inversions can cause centromere shifts. h, Example of how a centromere remains at or near to its original ___location after a segment is moved by an inversion.