Cytoduction Preserves Genetic Diversity Following Plasmid Transfer Into Pooled Yeast Libraries

Introducing plasmids into yeast is a critical step for many phenotypic assays and genetic engineering applications. However, it is often challenging for applications that involve large pools of variants because the population structure can be easily altered by traditional methods such as chemical transformation. In this study, we introduce drug-marked plasmids into a heterogeneous yeast population using both transformation and cytoduction (mating without nuclear fusion). Using a highly diverse barcoded yeast collection, we quantify the efficiency of both methods. We demonstrate that for cytoduction, but not transformation, nearly all the genotypes in the initial pool were detected in the final pool, with a high correlation to their initial frequencies. Finally, we map QTL that impact both cytoduction and transformation. Overall, we demonstrate the efficiency of cytoduction as a means of introducing plasmids into yeast. This is significant because it provides a means of manipulating diverse yeast populations, such as pools constructed for bulk segregant analysis, deep mutational scanning, large-scale gene editing, or populations from long-term evolution experiments.