High-resolution single-cell sequencing of malaria parasites.

Single-cell genomics is a powerful tool for determining the genetic architecture of complex communities of unicellular organisms. In areas of high transmission, malaria patients are often challenged by the activities of multiple Plasmodium falciparum lineages, which can potentiate pathology, spread drug resistance loci and also complicate most genetic analysis. Single-cell sequencing of P. falciparum would be key to understanding infection complexity, though efforts are hampered by the extreme nucleotide composition of its genome (∼80% AT-rich). To counter the low coverage achieved in previous studies, we found that accurate, near-complete single-cell genome capture is possible by targeting DNA-rich late-stage parasites by Fluoresence-Activated Cell Sorting and whole genome sequencing. Our method routinely generates near-complete capture of the 23Mb P. falciparum genome (mean breadth of coverage 90.7%) at high efficiency. Data from 48 single-cell genomes derived from a polyclonal infection sampled in Chikhwawa, Malawi allowed for unambiguous determination of haplotype diversity and recent meiotic events, information that will aid public health efforts. [Abstract copyright: © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.]