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High-resolution single-cell sequencing of malaria parasites

View ORCID ProfileSimon G. Trevino, Standwell C. Nkhoma, Shalini Nair, Benjamin J. Daniel, Karla Moncada, Stanley Khoswe, Rachel L. Banda, View ORCID ProfileFrançois Nosten, View ORCID ProfileIan H. Cheeseman
doi: https://doi.org/10.1101/130864
Simon G. Trevino
1Texas Biomedical Research Institute, San Antonio, Texas 78227-5301, USA
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  • For correspondence: strevino@txbiomed.org
Standwell C. Nkhoma
2Malawi-Wellcome-Liverpool-Wellcome Trust Clinical Research Programme, PO Box 30096, Chichiri, Blantyre 3, Malawi
3Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
4Wellcome Trust Liverpool Glasgow Centre for Global Health Research, 70 Pembroke Place, Liverpool, L69 3GF, UK
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Shalini Nair
1Texas Biomedical Research Institute, San Antonio, Texas 78227-5301, USA
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Benjamin J. Daniel
5University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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Karla Moncada
5University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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Stanley Khoswe
2Malawi-Wellcome-Liverpool-Wellcome Trust Clinical Research Programme, PO Box 30096, Chichiri, Blantyre 3, Malawi
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Rachel L. Banda
2Malawi-Wellcome-Liverpool-Wellcome Trust Clinical Research Programme, PO Box 30096, Chichiri, Blantyre 3, Malawi
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François Nosten
6Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak 63110, Thailand
7Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
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Ian H. Cheeseman
1Texas Biomedical Research Institute, San Antonio, Texas 78227-5301, USA
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  • For correspondence: ianc@txbiomed.org
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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 23Mb P. falciparum genome (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.

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Posted May 04, 2017.
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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
bioRxiv 130864; doi: https://doi.org/10.1101/130864
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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
bioRxiv 130864; doi: https://doi.org/10.1101/130864

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