Whole genome rearrangement of Saccharomyces cerevisiae with SCRaMbLE

SCRaMbLE-mediated whole genome engineering by introducing large amounts of genetic diversity is desired for biotechnological applications and genome decoding but has not been actually demonstrated. Here, an efficient platform named Multiplex and consecutive Genome engineering and induced evolution (McGee) was developed to simultaneously insert short DNA sequences, for example, the loxPsym site, into the yeast genome. 83 loxPsym sites across all 16 chromosomes were integrated by McGee, which further mediated genome-wide large fragment rearrangements by Cre expression, revealing some interesting features of this system. Analysis of rearranged strains revealed the complex impacts of large genome rearrangements on phenotypes, transcription, and 3D genome structure.