Fig. 3

Sequences immunoprecipitated with CENP-A are enriched at the center of the chromosome. a Short-read sequences from a chromatin-immunoprecipitation (ChIP-seq) with CENP-A were aligned to the reference Y chromosome assembly. There is a prominent peak between markers STN187 and WT1A where the centromere is located. CENP-A enrichment from a second male fish is shown in (Additional file 2: Fig. S8). b Alpha satellite monomeric repeats are organized into higher order repeats (HORs). Sequence identity is shown in 100 bp windows across the centromere sequence of the Y chromosome. 87 kb of sequence containing the monomeric repeat was rejoined (crosshatched) to contigs that were previously fragmented in the scaffolding process (orange contig: 11,894; yellow contig: 11,839). The gap between the two contigs is shown in gray