Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum

Gene

Volumn 387, Issue 1-2, 2007, Pages 1-6

  Volkman, Sarah K ^a   Lozovsky, Elena ^b   Barry, Alyssa E ^c   Bedford, Trevor ^b   Bethke, Lara ^a   Myrick, Alissa ^a   Day, Karen P ^c   Hartl, Daniel L ^b   Wirth, Dyann F ^a   Sawyer, Stanley A ^d  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b HARVARD UNIVERSITY   (United States)

^c NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d WASHINGTON UNIVERSITY   (United States)

Author keywords

Coalescent analysis; Genetic diversity; Malaria

Indexed keywords

MICROSATELLITE DNA; OLIGONUCLEOTIDE;

ARTICLE; BASE PAIRING; CHROMOSOME 2; CHROMOSOME 3; DNA FLANKING REGION; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCATION; GENE LOCUS; GENE MAPPING; GENETIC CODE; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HYBRIDIZATION; INTRON; MALARIA; NONHUMAN; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; DNA, PROTOZOAN; GENES, PROTOZOAN; GENOME, PROTOZOAN; MICROSATELLITE REPEATS; PLASMODIUM FALCIPARUM; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTOZOAN PROTEINS; VARIATION (GENETICS);

PLASMODIUM FALCIPARUM;

EID: 33845639625     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.07.026     Document Type: Article

References (35)

1. Barry A.E., Leliwa A., Choi M., Nielsen K.M., Hartl D.L., and Day K.P. DNA sequence artifacts and the estimation of time to the most recent common ancestor (TMRCA) of Plasmodium falciparum. Mol. Biochem. Parasitol. 130 (2003) 143-147
2. Barry A.E., et al. Variable SNP density in aspartyl-protease genes of the malaria parasite Plasmodium falciparum. Gene 376 (2006) 163-173
3. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27 (1999) 573-580
4. Biggs B.A., et al. Antigenic variation in Plasmodium falciparum. Proc. Natl. Acad. Sci. U. S. A. 88 (1991) 9171-9174
5. Biswas S., Escalante A., Chaiyaroj S., Angkasekwinai P., and Lal A.A. Prevalence of point mutations in the dihydrofolate reductase and dihydropteroate synthetase genes of Plasmodium falciparum isolates from India and Thailand: a molecular epidemiologic study. Trop. Med. Int. Health 5 (2000) 737-743
6. Bruce-Chwatt L.J. A longitudinal survey of natural malaria infection in a group of West African adults. West Afr. Med. J. 12 (1963) 199-217
7. Conway D.J., et al. High recombination rate in natural populations of Plasmodium falciparum. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 4506-4511
8. Fidock D.A., et al. Mutations in the P. falciparum digestive vacuole transmembrane protein PfCRT and evidence for their role in chloroquine resistance. Mol. Cell 6 (2000) 861-871
9. Foote S.J., Thompson J.K., Cowman A.F., and Kemp D.J. Amplification of the multidrug resistance gene in some chloroquine-resistant isolates of P. falciparum. Cell 57 (1989) 921-930
10. Foote S.J., et al. Several alleles of the multidrug-resistance gene are closely linked to chloroquine resistance in Plasmodium falciparum. Nature 345 (1990) 255-258
11. Griffiths R.C., and Tavare S. Ancestral inference in population genetics. Stat. Sci. 9 (1994) 307-319
12. Griffiths R.C., and Tavare S. Unrooted genealogical tree probabilities in the infinitely-many-sites model. Math. Biosci. 127 (1995) 77-98
13. Holder A.A., and Freeman R.R. Protective antigens of rodent and human bloodstage malaria. Philos. Trans. R. Soc. Lond., B Biol. Sci. 307 (1984) 171-177
14. Hughes A.L. Adaptive Evolution of Genes and Genomes (1999), Oxford University Press, New York
15. Kemp D.J., Cowman A.F., and Walliker D. Genetic diversity in Plasmodium falciparum. Adv. Parasitol. 29 (1990) 75-149
16. Marsh K. Malaria-a neglected disease?. Parasitology 104 (1992) S53-S69 (Suppl)
17. Miller L.H., Roberts T., Shahabuddin M., and McCutchan T.F. Analysis of sequence diversity in the Plasmodium falciparum merozoite surface protein-1 (MSP-1). Mol. Biochem. Parasitol. 59 (1993) 1-14
18. Mu J., et al. Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature 418 (2002) 323-326
19. Mu J., et al. Recombination hotspots and population structure in Plasmodium falciparum. PLoS Biol. 3 (2005) 1734-1741
20. Myrick A., Munasinghe A., Patankar S., and Wirth D.F. Mapping of the Plasmodium falciparum multidrug resistance gene 5′-upstream region, and evidence of induction of transcript levels by antimalarial drugs in chloroquine sensitive parasites. Mol. Microbiol. 49 (2003) 671-683
21. Nair S., et al. A selective sweep driven by pyrimethamine treatment in Southeast Asian malaria parasites. Mol. Biol. Evol. 20 (2003) 1526-1536
22. Neva F.A. Looking back for a view of the future: observations on immunity to induced malaria. Am. J. Trop. Med. Hyg. 26 (1977) 211-215
23. Nielsen K.M., et al. Gene conversion as a source of nucleotide diversity in Plasmodium falciparum. Mol. Biol. Evol. 20 (2003) 726-734
24. Peterson D.S., Milhous W.K., and Wellems T.E. Molecular basis of differential resistance to cycloguanil and pyrimethamine in Plasmodium falciparum malaria. Proc. Natl. Acad. Sci. U. S. A. 87 (1990) 3018-3022
25. Rich S.M., Licht M.C., Hudson R.R., and Ayala F.J. Malaria's Eve: evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 4425-4430
26. Roper C., et al. Antifolate antimalarial resistance in southeast Africa: a population-based analysis. Lancet 361 (2003) 1174-1181
27. Roper C., Pearce R., Nair S., Sharp B., Nosten F., and Anderson T. Intercontinental spread of pyrimethamine-resistant malaria. Science 305 (2004) 1124
28. Snounou G., et al. Biased distribution of msp1 and msp2 allelic variants in Plasmodium falciparum populations in Thailand. Trans. R. Soc. Trop. Med. Hyg. 93 (1999) 369-374
29. Su X., Kirkman L.A., Fujioka H., and Wellems T.E. Complex polymorphisms in an approximately 330 kDa protein are linked to chloroquine-resistant P. falciparum in Southeast Asia and Africa. Cell 91 (1997) 593-603
30. Su X., et al. A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum. Science 286 (1999) 1351-1353
31. Tanabe K., Mackay M., Goman M., and Scaife J.G. Allelic dimorphism in a surface antigen gene of the malaria parasite Plasmodium falciparum. J. Mol. Biol. 195 (1987) 273-287
32. Volkman S.K., et al. Recent origin of Plasmodium falciparum from a single progenitor. Science 293 (2001) 482-484
33. Wang P., Read M., Sims P.F., and Hyde J.E. Sulfadoxine resistance in the human malaria parasite Plasmodium falciparum is determined by mutations in dihydropteroate synthetase and an additional factor associated with folate utilization. Mol. Microbiol. 23 (1997) 979-986
34. Wilson C.M., Serrano A.E., Wasley A., Bogenschutz M.P., Shankar A.H., and Wirth D.F. Amplification of a gene related to mammalian mdr genes in drug-resistant Plasmodium falciparum. Science 244 (1989) 1184-1186
35. Wootton J.C., et al. Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum. Nature 418 (2002) 320-323