Fig. 3

Synteny and sequence similarity of the Pgt centromeres. A Regions of macro-synteny (> 20 kbp) between the haplotypes of chromosomes 1 and 2. For chromosome 1, the centromeric regions show no conservation whereas on chromosome 2 the centromeric regions are conserved as confirmed by B genomic dot plot alignments of the centromeric regions. C Clustering of k-mer distance estimations between centromeric and non-centromeric regions. The non-centromeric regions cluster as expected according to haplotypes. In contrast, the centromeric regions are highly divergent, even between haplotypes