De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture
Fig 4
Recovery of telomeres and identification of putative centromere repeats for each chromosome.
A. Presence of telomere repeats at or near the ends of most chromosome arms. Shown is enrichment of telomere repeats and H3K9me3 marks in 10-kb nonoverlapping sliding windows. B. Alignment of chromosome ends and telomere repeats. Colors indicate the percent similarity between the alignments and the direction of the lines indicates the direction of the match. C. Histogram of most abundant satellites in Drosophila miranda genome. Repeat categories refer to the size of the repeat unit. Note that the 84-bp repeat is a higher-order variant of four units of the 21-bp repeat. D. Consensus sequence of 21-bp and 99-bp repeats. Gray shading indicates AA/TT/AT repeats that occur at a 10-bp periodicity. E. Comparison of the centromeric repeat from different chromosomes. Shown are alignments of regions from Muller B and Muller C, with high density of the 99-bp and 21-bp tandem centromeric repeats, respectively. F. Location of putative centromere repeats in pericentromeric regions, and H3K9me3 enrichment. H3K9me3 enrichment is reduced at the putative centromeric repeats (S13 Fig). Note that, for the acrocentric chromosome 2, we recover the entire centromere, including the telomere. ch, chromosome; H3K9me3, trimethylation of histone 3 lysine 9; TE, transposable element.