Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects

Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic <i>Saccharomyces cerevisiae</i> genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of <i>S. cerevisiae</i> chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased <i>TAR1</i> copy number. We also extended the utility of the synthetic chromosome recombination and modification by <i>loxP</i>sym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the <i>S. cerevisiae</i> genome in the presence of rational and non-rational modifications.