Figure 3

Structural rearrangement and breakpoint information in the amplification of the SUL1 locus. Top: Sequence reads from the evolved genome spanning the breakpoints of the chromosome 2 amplification (black and white arrow with red and green ends) are shown aligned to the wild-type genomic sequences at these termini. These reads support the presence of the wild-type sequences at the borders of the amplified segment: 'Evo L' (red) and 'Evo R' (green) ends. The positions of inverted repeats in the yeast genome are highlighted in white squares (with black arrow heads) with the corresponding coordinates from chromosome 2. Underlined bases in the right-end contigs and reads indicate positions where inverted repeats differ. Middle: Contigs of unmapped reads shown in red ('Evo I') and green ('Evo II') consist of chromosome 2 genomic sequences from the borders of amplification but contain an inversion breakpoint. Arrows indicate directionality of the subgenomic sequences composing these contigs. Black sequences correspond to the nearby inverted repeats in the reference genome. Coordinates of the regions of identity to the reference chromosome 2 are indicated below each contig. Left-end breakpoints ('Evo I') are composed of chr2: 784,010-784,035 and chr2: 784,028-784,060 subsequences inverted with a 7 nt overlap. Right-end breakpoints ('Evo II") are composed of chr2: 795,082-795,113 and chr2: 795,137-795,168 subsequences inverted with a 13 nt overlap. Bottom: Contig composition and the presence of reads spanning the wild-type sequences at the boundaries of the amplification support inverted rearrangements as the structure underlying the 5× amplification along chromosome 2.