Fig. 1: Hi-C-assisted assembly of chromosome-scale scaffolds for S. microadriaticum.

a, Main steps in Hi-C-assisted assembly of Smic1.0 and Smic1.1N. b, Hi-C interaction map for the set of 94 chromosomes (ordered by descending size, 250-kb bins) of Smic1.0 and 94 clusters of high-copy scaffolds (ordered according to their preferred interactions with the set of 94 chromosomes). Relative sequence coverage per 10-kb bin is shown along the right axis. Each of the clusters interact mostly with only one of the chromosomes, but sequences in these clusters have, on average, a copy number that is 11 times higher than sequences located along the assembled portions of chromosomes 1–94. c, Examples of Hi-C interaction maps for chromosomes 4, 26 and 59. Hi-C data are mapped to Smic1.0 and binned at 50-kb resolution. Dotted squares indicate sections that are shown at higher resolution (5-kb bins) below the chromosome-wide interaction maps. Plots on top of the heatmaps represent insulation profiles (10-kb resolution, window size 500 kb; Methods). This profile represents the number of interactions that occur across each location. Local minima in these profiles indicate the locations of sites across which interaction frequencies are relatively low, and these correspond to Hi-C domain boundaries.