SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes

Sequencing of reduced representation libraries enables genotyping of many individuals for population genomic studies. However, high amounts of DNA are required, and the method cannot be applied directly on single cells, preventing its use on most microbes. We developed and implemented the analysis of single amplified genomes followed by restriction-site-associated DNA sequencing to bypass labor-intensive culturing and to avoid culturing bias in population genomic studies of unicellular eukaryotes. This method thus opens the way for addressing important questions about the genetic diversity, gene flow, adaptation, dispersal, and biogeography of hitherto unexplored species.

Automated summary

Sequencing of reduced representation libraries allows for genotyping of many individuals in population genomic studies. However, it cannot be applied directly on single cells and requires high amounts of DNA, which limits its use on most microbes. To address this limitation, we developed a method called single amplified genomes followed by restriction-site-associated DNA sequencing, which avoids labor-intensive culturing and culturing bias, enabling population genomic studies on unicellular eukaryotes and providing insights into genetic diversity, gene flow, adaptation, dispersal, and biogeography of previously unexplored species.