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Adaptive copy number evolution in malaria parasites.

Nair S, Miller B, Barends M, Jaidee A, Patel J, Mayxay M, Newton P, Nosten F, Ferdig MT, Anderson TJ - PLoS Genet. (2008)

Bottom Line: The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP.These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function.More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation.

View Article: PubMed Central - PubMed

Affiliation: Southwest Foundation for Biomedical Research (SFBR), San Antonio, TX, USA.

ABSTRACT
Copy number polymorphism (CNP) is ubiquitous in eukaryotic genomes, but the degree to which this reflects the action of positive selection is poorly understood. The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP. We provide compelling evidence that gch1 CNP is an adaptive consequence of selection by antifolate drugs, which target enzymes downstream in this pathway. (1) We compared gch1 CNP in parasites from Thailand (strong historical antifolate selection) with those from neighboring Laos (weak antifolate selection). Two percent of chromosomes had amplified copy number in Laos, while 72% carried multiple (2-11) copies in Thailand, and differentiation exceeded that observed at 73 synonymous SNPs. (2) We found five amplicon types containing one to greater than six genes and spanning 1 to >11 kb, consistent with parallel evolution and strong selection for this gene amplification. gch1 was the only gene occurring in all amplicons suggesting that this locus is the target of selection. (3) We observed reduced microsatellite variation and increased linkage disequilibrium (LD) in a 900-kb region flanking gch1 in parasites from Thailand, consistent with rapid recent spread of chromosomes carrying multiple copies of gch1. (4) We found that parasites bearing dhfr-164L, which causes high-level resistance to antifolate drugs, carry significantly (p = 0.00003) higher copy numbers of gch1 than parasites bearing 164I, indicating functional association between genes located on different chromosomes but linked in the same biochemical pathway. These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function. More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation.

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Geographical differentiation of the gch1 CNP.The frequency of chromosomes carrying different gch1 copy number is plotted in Thailand (a) and Laos (b). (c) Map showing sampling locations in Thailand and Laos. The pie charts show the representation of alleles present at known genes involved in antifolate resistance, and provides a molecular indicator of the strength of antifolate selection on these two populations. White-wild type, yellow-1 mutation, orange-2 mutations, red-3 mutations, black-4 mutations. See table S5 for details of the alleles present. (d) The distribution of FST for gch1 CNP and for 73 polymorphic sSNPs. The markers are plotted by position across the genome. The mean FST for sSNPs is marked by the dotted line.
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pgen-1000243-g003: Geographical differentiation of the gch1 CNP.The frequency of chromosomes carrying different gch1 copy number is plotted in Thailand (a) and Laos (b). (c) Map showing sampling locations in Thailand and Laos. The pie charts show the representation of alleles present at known genes involved in antifolate resistance, and provides a molecular indicator of the strength of antifolate selection on these two populations. White-wild type, yellow-1 mutation, orange-2 mutations, red-3 mutations, black-4 mutations. See table S5 for details of the alleles present. (d) The distribution of FST for gch1 CNP and for 73 polymorphic sSNPs. The markers are plotted by position across the genome. The mean FST for sSNPs is marked by the dotted line.

Mentions: Comparing patterns of geographical differentiation in neutral and putatively selected loci provides a powerful approach to identify loci that underlie adaptation [25],[40],[41]. This approach is based on the premise that allele distribution at neutrally evolving loci will be determined by mutation and drift alone, while selection will influence patterns observed at loci involved in adaptation. We measured gch1 copy number in parasites from Phalanxay (Southern Laos) for comparison with Thailand. These neighboring countries differ considerably in history of antifolate treatment [25],[27]. In Thailand, there was intensive selection with antifolates from 1970–1980 [42], whereas in Laos antifolates were the official second line treatment for malaria until 2006, but in reality they were very seldom used [26]. Differences in treatment policies and antifolate selection are evident from patterns of polymorphism at dhfr and dhps. All parasite samples (n = 139) examined from Thailand carried between 2 and 4 mutations at dhfr, and 80% of parasite isolates carried the dhfr-164L mutation, while at dhps all Thai parasites carried 2 or 3 mutations conferring resistance (Figure 3, Table S5). In contrast, in Laos the dhfr-164L mutation was absent, and 23% of parasites carried wild type dhfr alleles, while 92% of parasites carried wild-type alleles at dhps (Figure 3, Table S5).


Adaptive copy number evolution in malaria parasites.

Nair S, Miller B, Barends M, Jaidee A, Patel J, Mayxay M, Newton P, Nosten F, Ferdig MT, Anderson TJ - PLoS Genet. (2008)

Geographical differentiation of the gch1 CNP.The frequency of chromosomes carrying different gch1 copy number is plotted in Thailand (a) and Laos (b). (c) Map showing sampling locations in Thailand and Laos. The pie charts show the representation of alleles present at known genes involved in antifolate resistance, and provides a molecular indicator of the strength of antifolate selection on these two populations. White-wild type, yellow-1 mutation, orange-2 mutations, red-3 mutations, black-4 mutations. See table S5 for details of the alleles present. (d) The distribution of FST for gch1 CNP and for 73 polymorphic sSNPs. The markers are plotted by position across the genome. The mean FST for sSNPs is marked by the dotted line.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2570623&req=5

pgen-1000243-g003: Geographical differentiation of the gch1 CNP.The frequency of chromosomes carrying different gch1 copy number is plotted in Thailand (a) and Laos (b). (c) Map showing sampling locations in Thailand and Laos. The pie charts show the representation of alleles present at known genes involved in antifolate resistance, and provides a molecular indicator of the strength of antifolate selection on these two populations. White-wild type, yellow-1 mutation, orange-2 mutations, red-3 mutations, black-4 mutations. See table S5 for details of the alleles present. (d) The distribution of FST for gch1 CNP and for 73 polymorphic sSNPs. The markers are plotted by position across the genome. The mean FST for sSNPs is marked by the dotted line.
Mentions: Comparing patterns of geographical differentiation in neutral and putatively selected loci provides a powerful approach to identify loci that underlie adaptation [25],[40],[41]. This approach is based on the premise that allele distribution at neutrally evolving loci will be determined by mutation and drift alone, while selection will influence patterns observed at loci involved in adaptation. We measured gch1 copy number in parasites from Phalanxay (Southern Laos) for comparison with Thailand. These neighboring countries differ considerably in history of antifolate treatment [25],[27]. In Thailand, there was intensive selection with antifolates from 1970–1980 [42], whereas in Laos antifolates were the official second line treatment for malaria until 2006, but in reality they were very seldom used [26]. Differences in treatment policies and antifolate selection are evident from patterns of polymorphism at dhfr and dhps. All parasite samples (n = 139) examined from Thailand carried between 2 and 4 mutations at dhfr, and 80% of parasite isolates carried the dhfr-164L mutation, while at dhps all Thai parasites carried 2 or 3 mutations conferring resistance (Figure 3, Table S5). In contrast, in Laos the dhfr-164L mutation was absent, and 23% of parasites carried wild type dhfr alleles, while 92% of parasites carried wild-type alleles at dhps (Figure 3, Table S5).

Bottom Line: The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP.These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function.More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation.

View Article: PubMed Central - PubMed

Affiliation: Southwest Foundation for Biomedical Research (SFBR), San Antonio, TX, USA.

ABSTRACT
Copy number polymorphism (CNP) is ubiquitous in eukaryotic genomes, but the degree to which this reflects the action of positive selection is poorly understood. The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP. We provide compelling evidence that gch1 CNP is an adaptive consequence of selection by antifolate drugs, which target enzymes downstream in this pathway. (1) We compared gch1 CNP in parasites from Thailand (strong historical antifolate selection) with those from neighboring Laos (weak antifolate selection). Two percent of chromosomes had amplified copy number in Laos, while 72% carried multiple (2-11) copies in Thailand, and differentiation exceeded that observed at 73 synonymous SNPs. (2) We found five amplicon types containing one to greater than six genes and spanning 1 to >11 kb, consistent with parallel evolution and strong selection for this gene amplification. gch1 was the only gene occurring in all amplicons suggesting that this locus is the target of selection. (3) We observed reduced microsatellite variation and increased linkage disequilibrium (LD) in a 900-kb region flanking gch1 in parasites from Thailand, consistent with rapid recent spread of chromosomes carrying multiple copies of gch1. (4) We found that parasites bearing dhfr-164L, which causes high-level resistance to antifolate drugs, carry significantly (p = 0.00003) higher copy numbers of gch1 than parasites bearing 164I, indicating functional association between genes located on different chromosomes but linked in the same biochemical pathway. These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function. More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation.

Show MeSH
Related in: MedlinePlus