High-Resolution Single-Cell Sequencing of Malaria Parasites

Simon G. Trevino, Standwell C. Nkhoma, Shalini Nair, Benjamin J. Daniel, Karla Moncada, Stanley Khoswe, Rachel L. Banda, François Nosten, Ian H. Cheeseman

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


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 (a 1/480% AT-rich). To counter the low coverage achieved in previous studies, we targeted DNA-rich late-stage parasites by Fluorescence-Activated Cell Sorting and whole genome sequencing. Our method routinely generates accurate, near-complete capture of the 23 Mb 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.

Original languageEnglish (US)
Pages (from-to)3373-3383
Number of pages11
JournalGenome Biology and Evolution
Issue number12
StatePublished - Dec 1 2017
Externally publishedYes


  • malaria
  • methods
  • single-cell genomics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


Dive into the research topics of 'High-Resolution Single-Cell Sequencing of Malaria Parasites'. Together they form a unique fingerprint.

Cite this