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Nat Genet DOI:10.1038/ng1930

A genome-wide map of diversity in Plasmodium falciparum.

Publication TypeJournal Article
Year of Publication2007
AuthorsVolkman, SK, Sabeti, PC, DeCaprio, D, Neafsey, DE, Schaffner, SF, Milner, DA, Daily, JP, Sarr, O, Ndiaye, D, Ndir, O, Mboup, S, Duraisingh, MT, Lukens, A, Derr, A, Stange-Thomann, N, Waggoner, S, Onofrio, R, Ziaugra, L, Mauceli, E, Gnerre, S, Jaffe, DB, Zainoun, J, Wiegand, RC, Birren, BW, Hartl, DL, Galagan, JE, Lander, ES, Wirth, DF
JournalNat Genet
Volume39
Issue1
Pages113-9
Date Published2007 Jan
ISSN1061-4036
KeywordsAfrica, Animals, Asia, Central America, Chromosome Mapping, Genetic Variation, Genome, Protozoan, Genotype, Humans, Phylogeny, Plasmodium falciparum, Polymorphism, Single Nucleotide, South America
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 (pi = 1.16 x 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.

URLhttp://dx.doi.org/10.1038/ng1930
DOI10.1038/ng1930
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/17159979?dopt=Abstract

Alternate JournalNat. Genet.
PubMed ID17159979
Grant ListK23 AI054518 / AI / NIAID NIH HHS / United States