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Sequence diversity and natural selection at domain I of the apical membrane antigen 1 among Indian Plasmodium falciparum populations.

Garg S, Alam MT, Das MK, Dev V, Kumar A, Dash AP, Sharma YD - Malar. J. (2007)

Bottom Line: The level of genetic diversity and diversifying selection were higher in Assam, Orissa, and Andaman and Nicobar Islands populations as compared to Uttar Pradesh and Goa.The amounts of gene flow among these populations were moderate.The data reported here will be valuable for the development of AMA1-based malaria vaccine.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India. sheenagarg2000@yahoo.com

ABSTRACT

Background: The Plasmodium falciparum apical membrane antigen 1 (AMA1) is a leading malaria vaccine candidate antigen. The complete AMA1 protein is comprised of three domains where domain I exhibits high sequence polymorphism and is thus named as the hyper-variable region (HVR). The present study describes the extent of genetic polymorphism and natural selection at domain I of the ama1 gene among Indian P. falciparum isolates.

Methods: The part of the ama1 gene covering domain I was PCR amplified and sequenced from 157 P. falciparum isolates collected from five different geographical regions of India. Statistical and phylogenetic analyses of the sequences were done using DnaSP ver. 4. 10. 9 and MEGA version 3.0 packages.

Results: A total of 57 AMA1 haplotypes were observed among 157 isolates sequenced. Forty-six of these 57 haplotypes are being reported here for the first time. The parasites collected from the high malaria transmission areas (Assam, Orissa, and Andaman and Nicobar Islands) showed more haplotypes (H) and nucleotide diversity pi as compared to low malaria transmission areas (Uttar Pradesh and Goa). The comparison of all five Indian P. falciparum subpopulations indicated moderate level of genetic differentiation and limited gene flow (Fixation index ranging from 0.048 to 0.13) between populations. The difference between rates of non-synonymous and synonymous mutations, Tajima's D and McDonald-Kreitman test statistics suggested that the diversity at domain I of the AMA1 antigen is due to positive natural selection. The minimum recombination events were also high indicating the possible role of recombination in generating AMA1 allelic diversity.

Conclusion: The level of genetic diversity and diversifying selection were higher in Assam, Orissa, and Andaman and Nicobar Islands populations as compared to Uttar Pradesh and Goa. The amounts of gene flow among these populations were moderate. The data reported here will be valuable for the development of AMA1-based malaria vaccine.

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A neighbor-joining (NJ) tree depicting the relationships between different AMA1 haplotypes observed among Indian P. falciparum populations. The distance matrix was prepared using Kimura 2-parameter evolutionary model. Alignment substitutions were considered for analysis while gaps were ignored. Numbers below the line indicate percentage bootstrap values for 1000 replications. The scale bar represents a genetic distance. The partial AMA1 sequence of P. reichenowi [AJ252087], the closet species to P. falciparum was taken as an out group [35].
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Figure 2: A neighbor-joining (NJ) tree depicting the relationships between different AMA1 haplotypes observed among Indian P. falciparum populations. The distance matrix was prepared using Kimura 2-parameter evolutionary model. Alignment substitutions were considered for analysis while gaps were ignored. Numbers below the line indicate percentage bootstrap values for 1000 replications. The scale bar represents a genetic distance. The partial AMA1 sequence of P. reichenowi [AJ252087], the closet species to P. falciparum was taken as an out group [35].

Mentions: Inter-population nucleotide differences (Kxy) varied from 8.3 (between UP and Goa) to 11.53 (Assam and A & N) (Table 3). Similarly, the average number of nucleotide (Dxy) and net nucleotide (Da) substitutions per site between populations ranged from 0.018 to 0.025 and 0.00135 to 0.0755 respectively (Table 3). Although Fst statistics for the whole Indian P. falciparum populations was found to be 0.085, the Fst values between different geographical populations varied from 0.048 (between Orissa and Goa) to 0.133 (between UP and Orissa) (Table 3). The phylogenetic analysis of the sequences revealed that only 14 AMA1 alleles were shared by more than one geographical area (Additional File 2). Therefore, no region-wise clustering of the alleles was observed (Figure 2). Inter-population comparison of the total (TM) versus shared (SM) number of mutations also showed similar pattern of genetic differentiation as maximum number of shared mutations were found between Orissa & Goa (19 of 41 mutations were shared), and Goa and A & N (18 of 37 mutations were shared) (Table 3). Thus the data on phylogeny and Fst indicated moderate level of genetic differentiation and thus a limited movement of genes between populations.


Sequence diversity and natural selection at domain I of the apical membrane antigen 1 among Indian Plasmodium falciparum populations.

Garg S, Alam MT, Das MK, Dev V, Kumar A, Dash AP, Sharma YD - Malar. J. (2007)

A neighbor-joining (NJ) tree depicting the relationships between different AMA1 haplotypes observed among Indian P. falciparum populations. The distance matrix was prepared using Kimura 2-parameter evolutionary model. Alignment substitutions were considered for analysis while gaps were ignored. Numbers below the line indicate percentage bootstrap values for 1000 replications. The scale bar represents a genetic distance. The partial AMA1 sequence of P. reichenowi [AJ252087], the closet species to P. falciparum was taken as an out group [35].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2211494&req=5

Figure 2: A neighbor-joining (NJ) tree depicting the relationships between different AMA1 haplotypes observed among Indian P. falciparum populations. The distance matrix was prepared using Kimura 2-parameter evolutionary model. Alignment substitutions were considered for analysis while gaps were ignored. Numbers below the line indicate percentage bootstrap values for 1000 replications. The scale bar represents a genetic distance. The partial AMA1 sequence of P. reichenowi [AJ252087], the closet species to P. falciparum was taken as an out group [35].
Mentions: Inter-population nucleotide differences (Kxy) varied from 8.3 (between UP and Goa) to 11.53 (Assam and A & N) (Table 3). Similarly, the average number of nucleotide (Dxy) and net nucleotide (Da) substitutions per site between populations ranged from 0.018 to 0.025 and 0.00135 to 0.0755 respectively (Table 3). Although Fst statistics for the whole Indian P. falciparum populations was found to be 0.085, the Fst values between different geographical populations varied from 0.048 (between Orissa and Goa) to 0.133 (between UP and Orissa) (Table 3). The phylogenetic analysis of the sequences revealed that only 14 AMA1 alleles were shared by more than one geographical area (Additional File 2). Therefore, no region-wise clustering of the alleles was observed (Figure 2). Inter-population comparison of the total (TM) versus shared (SM) number of mutations also showed similar pattern of genetic differentiation as maximum number of shared mutations were found between Orissa & Goa (19 of 41 mutations were shared), and Goa and A & N (18 of 37 mutations were shared) (Table 3). Thus the data on phylogeny and Fst indicated moderate level of genetic differentiation and thus a limited movement of genes between populations.

Bottom Line: The level of genetic diversity and diversifying selection were higher in Assam, Orissa, and Andaman and Nicobar Islands populations as compared to Uttar Pradesh and Goa.The amounts of gene flow among these populations were moderate.The data reported here will be valuable for the development of AMA1-based malaria vaccine.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India. sheenagarg2000@yahoo.com

ABSTRACT

Background: The Plasmodium falciparum apical membrane antigen 1 (AMA1) is a leading malaria vaccine candidate antigen. The complete AMA1 protein is comprised of three domains where domain I exhibits high sequence polymorphism and is thus named as the hyper-variable region (HVR). The present study describes the extent of genetic polymorphism and natural selection at domain I of the ama1 gene among Indian P. falciparum isolates.

Methods: The part of the ama1 gene covering domain I was PCR amplified and sequenced from 157 P. falciparum isolates collected from five different geographical regions of India. Statistical and phylogenetic analyses of the sequences were done using DnaSP ver. 4. 10. 9 and MEGA version 3.0 packages.

Results: A total of 57 AMA1 haplotypes were observed among 157 isolates sequenced. Forty-six of these 57 haplotypes are being reported here for the first time. The parasites collected from the high malaria transmission areas (Assam, Orissa, and Andaman and Nicobar Islands) showed more haplotypes (H) and nucleotide diversity pi as compared to low malaria transmission areas (Uttar Pradesh and Goa). The comparison of all five Indian P. falciparum subpopulations indicated moderate level of genetic differentiation and limited gene flow (Fixation index ranging from 0.048 to 0.13) between populations. The difference between rates of non-synonymous and synonymous mutations, Tajima's D and McDonald-Kreitman test statistics suggested that the diversity at domain I of the AMA1 antigen is due to positive natural selection. The minimum recombination events were also high indicating the possible role of recombination in generating AMA1 allelic diversity.

Conclusion: The level of genetic diversity and diversifying selection were higher in Assam, Orissa, and Andaman and Nicobar Islands populations as compared to Uttar Pradesh and Goa. The amounts of gene flow among these populations were moderate. The data reported here will be valuable for the development of AMA1-based malaria vaccine.

Show MeSH
Related in: MedlinePlus