Fig. 1

Schematic illustration of the SCRaMbLE-based genome compaction (SGC) method. The first step in SGC is to integrate the URA3 reporter into a nonessential LU. After SCRaMbLE, the cells are plated onto 5-FOA medium to select strains missing the URA3 reporter, within which rearrangements at other loci are highly likely to exist, as we reported previously [30]. The genomes of 5-FOA resistant strains are analyzed using PCRtags, followed by whole genome sequencing to identify sequence changes. Strains with the most synthetic sequences deleted are subjected to the next round of SGC