Abstract

Genetic variation allows the malaria parasite Plasmodium falciparum to overcome chemotherapeutic agents, vaccines and vector control strategies and remain a leading cause of global morbidity and mortality1. Here we describe an initial survey of genetic variation across the P. falciparum genome. We performed extensive sequencing of 16 geographically diverse parasites and identified 46,937 SNPs, demonstrating rich diversity among P. falciparum parasites (π = 1.16 × 10−3) and strong correlation with gene function. We identified multiple regions with signatures of selective sweeps in drug-resistant parasites, including a previously unidentified 160-kb region with extremely low polymorphism in pyrimethamine-resistant parasites. We further characterized 54 worldwide isolates by genotyping SNPs across 20 genomic regions. These data begin to define population structure among African, Asian and American groups and illustrate the degree of linkage disequilibrium, which extends over relatively short distances in African parasites but over longer distances in Asian parasites. We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite.

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Acknowledgements

We thank all members of the sample collection team in Senegal (A. Ahouidi, L. Ndiaye, O. Ly, Y. Diedhiou, T. Sene, A. Mbaye and D. Diop). We thank T. Taylor, K. Seydel, J. Montgomery, E. Dembo, M. Molyneux and S. Rogerson for help collecting the samples from Malawi. We also thank all the members of the Broad Sequencing Platform and M. Koehrsen, D. Richter and O. Shamovsky for sequence analysis help. Our thanks to M. Goyette and T. Rachupka for help with Sequenom genotyping. Thanks to N. Mahesh and G. Ramirez for help with sample preparation and parasite cultures and to J. Mu and X. Su for typing samples. We thank MR4 for providing us with malaria parasites contributed by the following depositors: W.E. Collins (MRA-347); D.E. Kyle (MRA-154, MRA-157, MRA-159, MRA-176, MRA-207, MRA-284, MRA-285); L.H. Miller and D. Baruch (MRA-331, MRA-326, MRA-328); W. Trager (MRA-731, MRA-732, MRA-733); D. Walliker (MRA-151, MRA-153, MRA-200); T.E. Wellems (MRA-155, MRA-156, MRA-309, MRA-464); and Y. Wu (MRA-201). Special thanks to J. Barnwell for providing P. reichenowi DNA. Our thanks to PlasmoDB (http://www.plasmodb.org) for access to the 3D7 genome sequence. The authors are supported by the US National Institutes of Health, SPARC funding of The Broad Institute of MIT and Harvard, the Burroughs-Wellcome Fund, The Bill and Melinda Gates Foundation, the NIAID Microbial Sequencing Center, the Ellison Medical Foundation, Fogarty International and the Exxon Mobil Foundation. P.C.S. is funded by the Damon Runyon Cancer Fellowship and the L'Oreal for Women in Science Award.

Author information

Author notes

    • Sarah K Volkman
    •  & Pardis C Sabeti

    These authors contributed equally to this work.

Affiliations

  1. Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA 02115.

    • Sarah K Volkman
    • , Danny A Milner Jr
    • , Johanna P Daily
    • , Manoj T Duraisingh
    • , Amanda Lukens
    •  & Dyann F Wirth
  2. The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 02142.

    • Pardis C Sabeti
    • , David DeCaprio
    • , Daniel E Neafsey
    • , Stephen F Schaffner
    • , Alan Derr
    • , Nicole Stange-Thomann
    • , Skye Waggoner
    • , Robert Onofrio
    • , Liuda Ziaugra
    • , Evan Mauceli
    • , Sante Gnerre
    • , David B Jaffe
    • , Joanne Zainoun
    • , Roger C Wiegand
    • , Bruce W Birren
    • , James E Galagan
    • , Eric S Lander
    •  & Dyann F Wirth
  3. Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, BP 7325 Dakar, Senegal.

    • Ousmane Sarr
    • , Daouda Ndiaye
    • , Omar Ndir
    •  & Soulyemane Mboup
  4. Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA 02138.

    • Daniel L Hartl
  5. Department of Biology, MIT, Cambridge, Massachusetts, USA 02139.

    • Eric S Lander
  6. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA 02142.

    • Eric S Lander
  7. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA 02115.

    • Eric S Lander

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Contributions

S.K.V. designed experiments, prepared samples, carried out Sequenom genotyping and PCR resequencing, analyzed genotyping data and wrote the paper. P.C.S. designed experiments; carried out Sequenom genotyping and PCR resequencing; analyzed data for linkage disequilibrium, allele frequency and long-range haplotypes and wrote the paper. D.D.C. analyzed sequence data, prepared sequence data for subsequent analysis and defined polymorphisms. D.E.N. analyzed data for allele frequency and nucleotide diversity by GO category. S.F.S. analyzed data for nucleotide diversity and selective sweeps. D.A.M., J.P.D., O.S., D.N., O.N., S.M. and M.T.D. helped with sample collection. J.P.D. and M.T.D. helped with culture adaptation. D.A.M. and A.L. helped with parasite cultures. A.D. helped with GO function analysis. N.S.-T. and J.Z. prepared libraries for sequencing. S.W. and R.O. helped with PCR resequencing. L.Z. helped with Sequenom genotyping. E.M., S.G. and D.B.J. created the genome assemblies for HB3 and Dd2. R.C.W. coordinated project flow. B.W.B. supervised sequencing. D.L.H. consulted on population genetic analysis. J.E.G. supervised and advised on sequence analysis. E.S.L. designed experiments, consulted on project outcomes and wrote the paper. D.F.W. designed experiments, coordinated all efforts, supervised project at all levels, consulted on project outcomes and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Dyann F Wirth.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Sample correspondence for SNPs.

  2. 2.

    Supplementary Fig. 2

    Separation of continental populations using genotyping SNPs.

  3. 3.

    Supplementary Fig. 3

    Allele frequency in spectra.

  4. 4.

    Supplementary Table 1

    Parasites used in the study.

  5. 5.

    Supplementary Table 2

    Twenty chromosomal regions selected for LD study.

  6. 6.

    Supplementary Table 3

    Nucleotide diversity across the genome.

  7. 7.

    Supplementary Table 4

    Comparison of genotyping from whole genome–amplified samples and the original unamplified sample.

  8. 8.

    Supplementary Methods

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DOI

https://doi.org/10.1038/ng1930

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