Single nucleotide polymorphisms, putatively neutral DNA markers and population genetic parameters in Indian Plasmodium vivax isolates

Parasitology

Volumn 137, Issue 12, 2010, Pages 1721-1730

  Gupta, Bhavna ^a   Dash, Aditya P ^b   Shrivastava, Nalini ^c   Das, Aparup ^a  

^a NATIONAL INSTITUTE OF MALARIA RESEARCH   (India)

^b WORLD HEALTH ORGANIZATION   (Switzerland)

^c JIWAJI UNIVERSITY   (India)

Author keywords

evolution; India; malaria; neutral markers; Plasmodium vivax; single nucleotide polymorphisms

Indexed keywords

DNA FRAGMENT; DNA MARKER; SPACER DNA;

ARTICLE; CONSERVATION GENETICS; DNA SEQUENCE; GENE SEQUENCE; INDIAN; INTRON; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITE ISOLATION; PLASMODIUM VIVAX; POPULATION GENETIC PARAMETERS; PRIORITY JOURNAL; PROTOZOAL GENETICS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SYNTENY; UNINDEXED SEQUENCE; VARIABLE NUMBER OF TANDEM REPEAT;

CHROMOSOME MAPPING; DNA, PROTOZOAN; EVOLUTION, MOLECULAR; GENETIC MARKERS; GENETICS, POPULATION; HUMANS; INDIA; MALARIA, VIVAX; PLASMODIUM VIVAX; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX;

EID: 78650511547     PISSN: 00311820     EISSN: 14698161     Source Type: Journal    
DOI: 10.1017/S0031182010000533     Document Type: Article

References (56)

1. Agapow, P. M. & Burt, A. (2001). Indices of multilocus linkage disequilibrium. Molecular Ecology Notes 1, 101-102. (Pubitemid 33691862)
2. Andolfatto, P. & Przeworski, M. (2001). Regions of lower crossing over harbor more rare variants in African populations of Drosophila melanogaster. Genetics 158, 657-665. (Pubitemid 32552305)
3. Baines, J. F., Das, A., Mousset, S. & Stephan, W. (2004). The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae. Genetics 168, 1987-1998. (Pubitemid 40066338)
4. Barrett, J. C., Fry, B., Maller, J. & Daly, M. J. (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265. (Pubitemid 40202029)
5. Begun, D.J. & Aquadro, C. F. (1992). Levels of naturally occurring DNA polymorphisms correlate with recombination rates in D. melanogaster. Nature, London 356, 519-520.
6. Braverman, J. M., Hudson, R. R., Kaplan, N. L., Langley, C. H. & Stephan, W. (1995). The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140, 783-796.
7. Brown, A. H. D., Feldman, M. W. & Nevo, E. (1980). Multilocus structure of natural populations of Hordeum spontaneum. Genetics 96, 523-536.
8. Carlton, J. M., Adams, J. H.,Silva,J. C.,Bidwell, S. L., Lorenzi, H., Caler, E., Crabtree, J., Anginoli, S. V., Merino, E. F., Amedeo, P., Cheng, Q., Conlson, R. M. R., Crabb, B. S., del Po, H. A., Essien, K., Feldblyum, T. V., Fernandez-Becerra, C., Gilson, P. R., Gueye, A. H., Guo Kang'a, S., Kooij, T. W. A., Korsinczky, M., Meyer, E. V.-S., Nene, V., Paulsen, I., White, O., Ralph, S. A., Ren, Q. & Sargeant, T. J. (2008 a). Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 455, 757-763.
9. Carlton, J. M., Escalante, A. A., Neafsey, D. & Volkman, S. K. (2008 b). Comparative evolutionary genomics of human malaria parasites. Trends in Parasitology 24, 545-550.
10. Cereb, N., Hughes, A. L. & Yang, S. Y. (1997). Locus-specific conservation of the HLA class I introns by intra-locus homogenization. Immunogenetics 47, 30-36. (Pubitemid 28062031)
11. Cole-Tobian, J. & King, C. L. (2003). Diversity and natural selection in Plasmodium vivax Duffy binding protein gene. Molecular and Biochemical Parasitology 127, 121-132. (Pubitemid 36369687)
12. Coombs, G. H., Goldberg, D. E., Klemba, M., Berry, C., Kay, J. & Mottram, J. C. (2001). Aspartic proteases of Plasmodium falciparum and other parasitic protozoa as drug targets. Trends in Parasitology 17, 532-537. (Pubitemid 34185360)
13. Cornejo, O. E. & Escalante, A. A. (2000). The origin and age of Plasmodium vivax. Trends in Parasitology 22, 558-563.
14. Cui, L., Escalante, A. A., Imwong, M. & Snounou, G. (2003). The genetic diversity of Plasmodium vivax populations. Trends in Parasitology 19, 220-226. (Pubitemid 36588596)
15. Das, A., Mohanty, S. & Stephan, W. (2004). Inferring the population structure and demography of Drosophila ananassae from multilocus data. Genetics 168, 1975-1985. (Pubitemid 40066337)
16. Das, A., Sharma, M., Gupta, B. & Dash, A. P. (2009). Plasmodium falciparum and P. vivax: so similar, yet very different. Parasitology Research 105, 1169-1171.
17. Fedorova, L. & Fedorov, A. (2003). Introns in gene evolution. Genetica 118, 123-131. (Pubitemid 36821044)
18. Feng, X., Carlton, J. M., Joy, D. A., Mu, J., Furuya, T., Suh, B. B., Wang, Y., Barnwell, J. W. & Su, X-Z. (2003). Single-nucleotide polymorphisms and genome diversity in Plasmodium vivax. Proceedings of the National Academy of Sciences, USA 100, 8502-8507. (Pubitemid 36842574)
19. Figtree, M., Pasay, C. J., Slade, R., Cheng, Q., Cloonan, N., Walker, J. & Saul, A. (2000). Plasmodium vivax synonymous substitution frequencies, evolution and population structure deduced from diversity in AMA1 and MSP1 genes. Molecular and Biochemical Parasitology 108, 53-66. (Pubitemid 30236315)
20. Fu, Y. X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915-925.
21. Fu, Y. X. & Li, W. H. (1993). Statistical tests of neutrality of mutations. Genetics 133, 693-709.
22. Grynberg, P., Fontes, C. J. F., Hughes, A. L. & Braga, E. M. (2008). Polymorphism at the apical membrane antigen 1 locus reflects the world population history of Plasmodium vivax. BMC Evolutionary Biology 8, 123. doi:10.1186/1471-2148-8-123 (Pubitemid 351725626)
23. Haubold, B., Travisano, M., Rainey, P. B. & Hudson, R. R. (1998). Detecting linkage disequilibrium in bacterial populations. Genetics 150, 1341-1348. (Pubitemid 28555540)
24. Hawkins, V. N., Auliff, A., Prajapati, S. K., Rungsihirunrat, K., Hapuarachchi, H. C., Maestre, A., O'Neil, M. T., Cheng, Q., Joshi, H., Na-Bangchang, K. & Sibley, C. H. (2008). Multiple origins of resistance-conferring mutations in Plasmodium vivax dihydrofolate reductase. Malaria Journal 7, 72. doi:10.1186/1475-2875-7-72 (Pubitemid 351679529)
25. Hudson, R. R. (1987). Estimating the recombination parameter of a finite population model without selection. Genetics Research Cambridge 50, 245-250.
26. Hughes, A. L. (2000). Evolution of introns and exons of class II MHC genes of vertebrates. Immunogenetics 51, 473-486.
27. Imwong, M., Nair, S., Pukrittayakamee, S., Sudimack, D., Williams, J. T., Mayxay, M., Newton, P. N., Jung, R. K., Nandy, A., Osorio, L., Carlton, J. M., White, N. J., Day, N. P. J. & Anderson, T. J. C. (2007) Contrasting genetic structure in Plasmodium vivax populations from Asia and South America. International Journal for Parasitology 37, 1013-1022. (Pubitemid 46887595)
28. Imwong, M., Pukrittayakamee, S., Cheng, Q., Moore, C., Looareesuwan, S., Snounou, G., White, N. J. & Day, N. P. J. (2005). Limited polymorphism in the dihydropteroate synthetase gene (dhps) of Plasmodium vivax isolates from Thailand. Antimicrobial Agents and Chemotherapy 49, 4393-4395. (Pubitemid 41400997)
29. Johnston, S. P., Pieniazek, N. J., Xayavong, M. V., Slemenda, S. B., Wilkins, P. P. & da Silva, A. J. (2006). PCR as a confirmatory technique for laboratory diagnosis of malaria. Journal of Clinical Microbiology 44, 1087-1089.
30. Jongwutiwes, S., Putaporntip, C., Iwasaki, T., Ferreira, M. U., Kanbara, H. & Hughes, A. L. (2005). Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax. Molecular Biology and Evolution 22, 1733-1739. (Pubitemid 41373584)
31. Jongwutiwes, S., Putaporntip, C., Friedman, R. & Hughes, A. L. (2002). The extent of nucleotide polymorphism is highly variable across a 3-kb region on Plasmodium falciparum chromosome 2. Molecular Biology and Evolution 19, 1585-1590. (Pubitemid 36752782)
32. Joshi, H., Valecha, N., Verma, A., Kaul, A., Mallick, P. K., Shalini, S., Prajapati, S. K., Sharma, S. K., Dev, V., Biswas, S., Nanda, N., Malhotra, M. S., Subbarao, S. K. & Dash, A. P. (2007). Genetic structure of Plasmodium falciparum field isolates in eastern and north-eastern India. Malaria Journal 6, 60. doi:10.1186/1475-2875-6-60 (Pubitemid 46917332)
33. Joshi, H., Subbarao, S. K., Adak, T., Nanda, N., Ghosh, S. K., Carter, R. & Sharma, V. P. (1997). Genetic structure of Plasmodium vivax isolates in India. Transactions of the Royal Society of Tropical Medicine and Hygiene 91, 231-235. (Pubitemid 27197304)
34. Joshi, H., Subbarao, S. K., Raghavendra, K. & Sharma, V. P. (1989). Plasmodium vivax: enzyme polymorphism in isolates of Indian origin. Transactions of the Royal Society of Tropical Medicine and Hygiene 83, 179-181. (Pubitemid 19265557)
35. Joy, D. A., Gonzalez-Ceron, L., Carlton, J. M., Gueye, A., Fay, M., McCutchan, T. F. & Su, X-Z. (2008). Local adaptation and vector-mediated population structure in Plasmodium vivax malaria. Molecular Biology and Evolution 25, 1245-1252.
36. Kim, J. R., Imwong, M., Nandy, A., Chotivanich, K., Nontprasert, A., Tonomsing, N., Maji, A., Addy, M., Day, N. P. J., White, N. & Pukrittayakamee, S. (2006). Genetic diversity of Plasmodium vivax in Kolkata, India. Malaria Journal 5, 71. doi:10.1186/1475-2875-5-71 (Pubitemid 44357748)
37. Leclerc, M. C., Durand, P., Gauthier, C., Patot, S., Billotte, N., Menegon, M., Severini, C., Ayala, F.J. & Renaud, F. (2004). Meager genetic variability of the human malaria agent Plasmodium vivax. Proceedings of the National Academy of Sciences, USA 101, 14455-14460. (Pubitemid 39346770)
38. Leclerc, M. C., Gauthier, C., Villegas, L. & Urdaneta, L. (2005). Genetic diversity of merozoite surface protein-1 gene of Plasmodium vivax isolates in mining villages of Venezuela (Bolivar State). Acta Tropica 95, 26-32. (Pubitemid 40805018)
39. Lim, C. S., Tazi, L. & Ayala, F. J. (2005). Plasmodium vivax: recent world expansion and genetic identity to Plasmodium simium. Proceedings of the National Academy of Sciences, USA 102, 15523-15528. (Pubitemid 41528090)
40. Mu, J., Joy, D. A., Duan, J., Huang, Y., Carlton, J., Walker, J., Barnwell, J., Beerli, P., Charleston, M. A., Pybus, O. G. & Su, X. Z. (2005). Host switches leads to emergence of Plasmodium vivax malaria in humans. Molecular Biology and Evolution 22, 1686-1693. (Pubitemid 41373579)
41. Na, B-K., Lee, E-G., Lee, H-W., Cho, S-H., Bae, Y-A., Kong, Y., Lee, J-K. & Kim, T-S. (2004). Aspartic proteases of Plasmodium vivax are highly conserved in wild isolates. Korean Journal of Parasitology 42, 61-66.
42. Nei, M. (1987). Molecular Evolutionary Genetics. Columbia University Press, New York, USA.
43. Parsch, J. (2003). Selective constraint on intron evolution in Drosophila. Genetics 165, 1843-1851. (Pubitemid 38040274)
44. Prajapati, S. K., Verma, A., Adak, T., Yadav, R. S., Kumar, A., Eapen, A., Das, M. K., Singh, N., Sharma, S. K., Rizvi, M. A., Dash, A. P. & Joshi, H. (2006). Allelic dimorphism of Plasmodium vivax gam-1 in the Indian subcontinent. Malaria Journal 5, 90. doi:10.1186/1475-2875-5-90. (Pubitemid 44691080)
45. Rajesh, V., Elamaran, M., Vidya, S., Gowrishankar, M., Kochar, D. & Das, A. (2007). Plasmodium vivax: genetic diversity of the apical membrane antigen-1 (AMA-1) in isolates from India. Experimental Parasitology 116, 252-256. (Pubitemid 46709894)
46. Rayner, J. C., Tran, T. M., Corredor, V., Huber, C. S., Barnwell, J. W. & Galinski, M. R. (2005). Dramatic difference in diversity between Plasmodium falciparum and Plasmodium vivax reticulocytes binding-like genes. American Journal of Tropical Medicine and Hygiene 72, 666-674. (Pubitemid 41278782)
47. Rozas, J., Sanchez-DelBarrio, J. C., Messeguer, X. & Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497. (Pubitemid 38016658)
48. Singh, V., Mishra, N., Awasthi, G., Dash, A. P. & Das, A. (2009). Why is it important to study malaria epidemiology in India? Trends in Parasitology 25, 452-457.
49. Tajima, F. (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437-460. (Pubitemid 14247444)
50. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595. (Pubitemid 19274682)
51. Thakur, A., Alam, M. T., Bora, H., Kaur, P. & Sharma, Y. D. (2008). Plasmodium vivax: Sequence polymorphism and effect of natural selection at apical membrane antigen 1 (PvAMA1) among Indian population. Gene 419, 35-42.
52. Vali, U., Brandstrom, M., Johansson, M. & Ellegren, H. (2008). Insertion-deletion polymorphisms (indels) as genetic markers in natural populations. BMC Genetics 9, 8. doi:10.1186/1471-2156-9-8.
53. Volkman, S. K., Barry, A. E., Lyons, E. J., Nielsen, K. M., Thomas, S. M., Choi, M., Thakore, S. S., Day, K. P., Wirth, D. F. & Hartl, D. L. (2001). Recent origin of Plasmodium falciparum from a single progenitor. Science 293, 482-484. (Pubitemid 32679073)
54. Watterson, G. (1975). On the number of segregation sites. Theoretical Population Biology 7, 256-276.
55. Weir, B. S. (1996). In Genetic Data Analysis II (ed. Austin, D. F.), pp. 216-216. Sinauer Associates, Sunderland, MA, USA. World Health Organization (2008). World malaria report. World Health Organization, Geneva, Switzerland.
56. Zhang, L-B. & Ge, S. (2007). Multilocus analysis of nucleotide variation and speciation in Oryza officinalis and its closer relatives. Molecular Biology and Evolution 24, 769-783. (Pubitemid 46355800)