RNA sequence (RNA-seq) profiling of SynIX strain

We describe the complete synthesis, assembly, debugging and characterization of a synthetic 404,963 bp yeast chromosome, synIX. Combined chromosome construction methods were used to synthesize the left arm of synIX (synIXL) and retrofit previously described synIXR. During synIX strain characterization, we identified and resolved a bug related to EST3, a gene involved in telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. We found that both synIX transfer via chromoduction and wild-type IX destabilization were efficient methods. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these two chromosomes. To assess the effects of synthetic genome design on gene expression levels, we performed mRNA sequencing of SynIX strain yLHM1601 against wildtype strain BY4741 at 30C and 37C.