High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq

Yeasts can be engineered into \"living foundries\" for non-natural chemical production by reprogramming their genome using a synthetic biology \"design-build-test\" cycle. While methods for \"design\" and \"build\" are scalable and efficient, \"test\" remains a labor-intensive bottleneck, limiting the effectiveness of the genetic reprogramming results. Here we describe Isogenic Colony Sequencing (ICO-seq), a massively-parallel strategy to assess the gene expression, and thus engineered pathway efficacy, of large numbers of genetically distinct yeast colonies. We use the approach to characterize opaque-white switching in 658 C. albicans colonies. By profiling transcriptomes of 1642 engineered S. cerevisiae strains, we use it to assess gene expression heterogeneity in a protein mutagenesis library. Our approach will accelerate synthetic biology by allowing facile and cost-effective transcriptional profiling of large numbers of genetically distinct yeast strains.