Fig. 2.

C. zofingiensis nuclear genome. The assembled sequence of the 19 chromosomes of the nuclear genome is shown (top bar in each pair) with the matching restriction fragment length fingerprint from the optical map (bottom bar in each pair). Nominal plus strands run 5′ to 3′ left to right. Thin vertical divisions mark BamHI sites (in silico in top bars, optical consensus in bottom bars). Lines from restriction sites on one bar to another indicate a maximally scoring alignment computed with a dynamic programming algorithm similar to that used in OpGen’s MapSolver software. Black squares at chromosome edges indicate sequence assembly has reached telomere-associated repeats. Thick horizontal orange bars indicate explicit assembly gaps (runs of Ns). Thick horizontal yellow bars indicate additional known assembly issues as cataloged in Dataset S4. Light blue background shading shows where alignments are not one-to-one; shading is light green otherwise. Red dots mark possible (peri)centromeric loci. The end of chromosome 5 is discussed in SI Appendix, SI Text, and ∼24× copies of the rDNA unit likely predominate at the beginning of the large sequence gap at the end of chromosome 13. Unplaced contigs/scaffolds and 24 copies of the rDNA unit are shown near the bottom right.