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High-resolution single-cell sequencing of malaria parasites
- Source :
- Genome Biology and Evolution
- Publication Year :
- 2017
-
Abstract
- Single-cell genomics is a powerful tool for determining the genetic structure of complex communities of unicellular organisms. Patients infected with the malaria-causing parasite,Plasmodium falciparum, often carry multiple, genetically distinct parasites. Little is known about the diversity and relatedness of these lineages. We have developed an improved single-cell genomics protocol to reconstruct individual haplotypes from infections, a necessary step in uncovering parasite ecology within the host. This approach captures singly-infected red blood cells (iRBCs) by fluorescence-activated cell sorting (FACS) prior to whole genome amplification (WGA) and whole genome sequencing (WGS). Here, we demonstrate that parasites in late cell cycle stages, which contain increased DNA content, are far superior templates for generating high quality genomic data. Targeting of these cells routinely generates near-complete capture of the 23MbP. falciparumgenome (mean breadth of coverage 90.7%) at high efficiency. We used this approach to analyze the genomes of 48 individual cells from a polyclonal malaria infection sampled in Chikhwawa, Malawi. This comprehensive dataset enabled high-resolution estimation of the clonality and the relatedness of parasite haplotypes within the infection, long-standing problems in malaria biology.
- Subjects :
- 0301 basic medicine
Malawi
Erythrocytes
Plasmodium falciparum
malaria
Genomics
Computational biology
Biology
Genome
Genetic analysis
Polymerase Chain Reaction
methods
03 medical and health sciences
0302 clinical medicine
parasitic diseases
Genetics
medicine
Humans
qu_460
Malaria, Falciparum
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
Whole Genome Amplification
Whole genome sequencing
0303 health sciences
single-cell genomics
Haplotype
Genetic Variation
DNA, Protozoan
medicine.disease
biology.organism_classification
3. Good health
wc_750
030104 developmental biology
Single cell sequencing
Haplotypes
qx_135
Child, Preschool
qu_450
Single-Cell Analysis
Genome, Protozoan
030217 neurology & neurosurgery
Malaria
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 17596653
- Volume :
- 9
- Issue :
- 12
- Database :
- OpenAIRE
- Journal :
- Genome Biology and Evolution
- Accession number :
- edsair.doi.dedup.....26ce920053c249d122d9853fb88dc023