Abstract The Sc2.0 project is building a eukaryotic synthetic genome from scratch, incorporating thousands of designer features. A major milestone has been achieved with the assembly of all individual Sc2.0 chromosomes. Here, we describe the consolidation of multiple synthetic chromosomes using endoreduplication intercross to generate a strain with 6.5 synthetic chromosomes. Genome-wide chromosome conformation capture and long-read direct RNA sequencing were performed on this strain to evaluate the effects of designer modifications, such as loxPsym site insertion, tRNA relocation, and intron deletion, on 3D chromosome organization and transcript isoform profiles. To precisely map “bugs”, we developed a method, CRISPR Directed Biallelic URA3 -assisted Genome Scan, or “CRISPR D-BUGS”, exploiting directed mitotic recombination in heterozygous diploids. Using this method, we first fine-mapped a synII defect resulting from two loxPsym sites in the 3’ UTR of SHM1 . This approach was also used to map a combinatorial bug associated with synIII and synX , revealing a highly unexpected genetic interaction that links transcriptional regulation, inositol metabolism and tRNA Ser CGA abundance. “Starvation” for tRNA Ser CGA leads to insufficient levels of the key positive inositol biosynthesis regulator, Swi3 , which contains tandem UCG codons. Finally, to expedite consolidation, we employed a new method, chromosome swapping, to incorporate the largest chromosome ( synIV ), thereby consolidating more than half of the Sc2.0 genome in a single strain.

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions