A novel high-throughput single-cell DNA sequencing method reveals hidden genomic heterogeneity in the unicellular eukaryote Leishmania

Genome instability is considered a major driver of adaptation in eukaryotic microorganisms, but its study is hampered by the limited availability of genomic technologies with single-cell resolution. Here we present a novel high throughput method to reconstruct both structural and nucleotide information at single-cell level in Leishmania, a protozoan parasite with a remarkable genome plasticity characterized by frequent gene copy number variations (CNVs) and high aneuploidy mosaicism. By combining the use of semi-permeable capsules with primary template-directed amplification, we could determine the karyotypes of hundreds of Leishmania parasites, detect distinct CNVs between different cell populations, and identify sub population of cells harboring distinct nucleotide variants, including in genes associated with drug resistance. This approach provides a powerful new framework to uncover hidden evolutionary potential in complex microbial populations, with application in studying adaptation, drug resistance, and genome evolution in Leishmania and other pathogens.