A genome-wide map of diversity in Plasmodium falciparum

Sarah K. Volkman, Pardis C. Sabeti, David Decaprio, Daniel E. Neafsey, Stephen F. Schaffner, Danny A. Milner, Johanna P. Daily, Ousmane Sarr, Daouda Ndiaye, Omar Ndir, Soulyemane Mboup, Manoj T. Duraisingh, Amanda Lukens, Alan Derr, Nicole Stange-Thomann, Skye Waggoner, Robert Onofrio, Liuda Ziaugra, Evan Mauceli, Sante GnerreDavid B. Jaffe, Joanne Zainoun, Roger C. Wiegand, Bruce W. Birren, Daniel L. Hartl, James E. Galagan, Eric S. Lander, Dyann F. Wirth

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230 Scopus citations

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 mortality. 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.

Original languageEnglish (US)
Pages (from-to)113-119
Number of pages7
JournalNature Genetics
Volume39
Issue number1
DOIs
StatePublished - Jan 1 2007
Externally publishedYes

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ASJC Scopus subject areas

  • Genetics

Cite this

Volkman, S. K., Sabeti, P. C., Decaprio, D., Neafsey, D. E., Schaffner, S. F., Milner, D. A., Daily, J. P., Sarr, O., Ndiaye, D., Ndir, O., Mboup, S., Duraisingh, M. T., Lukens, A., Derr, A., Stange-Thomann, N., Waggoner, S., Onofrio, R., Ziaugra, L., Mauceli, E., ... Wirth, D. F. (2007). A genome-wide map of diversity in Plasmodium falciparum. Nature Genetics, 39(1), 113-119. https://doi.org/10.1038/ng1930