Cenhaps on Chromosome 8. (A) Alignments between NAM lines and B73 over Chromosome 8. Syntenic aligned regions (gray) and inverted segments (red) are shown. Blue arrows show the cenhap region with exceptional divergence. (B) Alignments between NAM lines and P39 over Chromosome 8. Annotation is the same as A. (C) Pairwise alignments and TE comparisons between CML322, CML52, and B73 over an ∼1 Mb region of Chromosome 8. Total kb of major TE families are shown below, in colors that match the annotation in the main panel (see Supplemental Fig. S9 for a more detailed view of TE subfamilies). This region does not include the CENH3 or CentC domains. (D) Pairwise alignments between NAM lines and B73 over CentC arrays on Chromosome 8. x- and y-axes show CentC monomers, and color intensity reflects the Jaccard index (JI) between each monomer pair. The non-B73 haplotypes are shaded in olive. (E) Clustering of CentC arrays on centromere 8. The colors over inbred names indicate varieties of corn: northern flint (pink), temperate (blue), mixed (red), and tropical (green).
