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

Published online by Cambridge University Press:  01 July 2010

BHAVNA GUPTA ,
ADITYA P. DASH ,
NALINI SHRIVASTAVA  and
APARUP DAS
BHAVNA GUPTA
Affiliation:
Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India
ADITYA P. DASH
Affiliation:
World Health Organization, Southeast Asian Regional Office, New Delhi, India
NALINI SHRIVASTAVA
Affiliation:
School of Studies in Biotechnology, Jiwaji University, Gwalior, Madhya Pradesh, India
APARUP DAS*
Affiliation:
Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India
*
*Corresponding author: Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India. Tel: +91 11 25307322. Fax: +91 11 25307 377. E-mail: aparup@mrcindia.org
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Summary

With a view to developing putatively neutral markers based on Single Nucleotide Polymorphisms (SNPs) in the human malaria parasite, Plasmodium vivax, we utilized the published whole genome sequence information of P. falciparum and P. vivax to find a ~200 kb conserved syntenic region between these two species. We have selected 27 non-coding DNA fragments (in introns and intergenic regions) of variable length (300–750 bp) in P. vivax in this syntenic region. PCR of P. vivax isolates of a population sample from India could successfully amplify 17 fragments. Subsequently, DNA sequencing and sequence analysis confirmed the polymorphic status of only 11 fragments. Altogether, 18 SNPs were detected and 2 different measures of nucleotide diversity showed variable patterns across different fragments; in general, introns were less variable than the intergenic regions. All 11 polymorphic fragments were found to be evolving according to a neutral equilibrium model and thus could be utilized as putatively neutral markers for population genetic studies in P. vivax. Different molecular population genetics parameters were also estimated, providing initial insight into the population genetics of Indian P. vivax.

Keywords

malariaIndiaPlasmodium vivaxneutral markerssingle nucleotide polymorphismsevolution
Type
Research Article
Information
Parasitology , Volume 137 , Issue 12 , October 2010 , pp. 1721 - 1730
Copyright
Copyright © Cambridge University Press 2010

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