Figure 2

A copy-number polymorphism harboring the SUL1 locus detected via whole genome sequencing. A) Circular binary segmentation of sequencing-depth ratios between evolved and parental genomes using DNAcopy. Gray dots represent the per nucleotide read-depth in the genome sequencing data. Segmentation-derived regions of equal copy number are indicated in red, smoothed by removing segments < 3× standard deviation apart. Segmentation defines a ~11 kb region with a 5.0× amplification and predicted breakpoints at chr2:784,043-795,080 (+/- 25 bp). The region of the sulfate permease SUL1 gene is shaded green. Blue lines indicate mappable positions in the reference genome. B) Array CGH data are shown for comparison. Tiling array data (gray dots) support a copy number amplification with breakpoints at 784009-795143 (+/- 50 nt). Blue line corresponds to the R runmed-smoothed trend in the data. A copy number estimate of 4.5× was obtained by comparative hybridization using ORF arrays (red lines). Tiling array hybridizations were optimized for SNP-calling and as such provide inaccurate copy number estimates.