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Genome Biol Evol. 2017 Dec 1;9(12):3373-3383. doi: 10.1093/gbe/evx256.

High-Resolution Single-Cell Sequencing of Malaria Parasites.

Author information

Genetics Department, Texas Biomedical Research Institute, San Antonio, Texas.
Malawi-Wellcome-Liverpool-Wellcome Trust Clinical Research Programme, Chichiri, Blantyre, Malawi.
Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, United Kingdom.
University of Texas Health Science Center at San Antonio, San Antonio, Texas.
Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand.
Nuffield Department of Medicine, Centre for Tropical Medicine, University of Oxford, United Kingdom.


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 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.


malaria; methods; single-cell genomics

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