Iterative SCRaMbLE for Engineering Synthetic Genome Modules and Chromosomes

The goal is to demonstrate how iterative cycles of SCRaMbLE (Synthetic Chromosome Recombination and Modification by LoxPsym-mediated Evolution) reorganises synthetic genome modules and chromosomes to improve functions. We introduce SCOUT (SCRaMbLE Continuous Output and Universal Tracker), a reporter system that allows sorting of SCRaMbLEd cells into high-diversity pools. Paired with long-read sequencing, SCOUT enables high-throughput mapping of genotype abundance and genotype-phenotype relationships.