Limits...
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.

Show MeSH

Related in: MedlinePlus

Haplotype structure and LD decay around gch1.(a) Plots of EHH for markers flanking gch1 from Thailand and Laos. In Thailand, EHH is plotted for the three predominant amplicon types (2.2, 7.3 and 8.7 kb). EHH for chromosomes with single copies of gch1 from both countries is shown for comparison. (b) Visual representation of LD. Microsatellite data was reduced to binary form by coloring the predominant allele in black and all other alleles in white. The 33 loci typed are arranged in order across the chromosome, while samples are arranged in rows. The country of origin of each sample is shown on the left, while the amplicon type (Figure 2) is shown on the right.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2570623&req=5

pgen-1000243-g005: Haplotype structure and LD decay around gch1.(a) Plots of EHH for markers flanking gch1 from Thailand and Laos. In Thailand, EHH is plotted for the three predominant amplicon types (2.2, 7.3 and 8.7 kb). EHH for chromosomes with single copies of gch1 from both countries is shown for comparison. (b) Visual representation of LD. Microsatellite data was reduced to binary form by coloring the predominant allele in black and all other alleles in white. The 33 loci typed are arranged in order across the chromosome, while samples are arranged in rows. The country of origin of each sample is shown on the left, while the amplicon type (Figure 2) is shown on the right.

Mentions: If chromosomes carrying gch1 CNP have been under strong recent selection in Thailand, we would predict that genetic diversity would be reduced and LD increased in the vicinity of gch1 on chr. 12. We measured length variation at 33 di-nucleotide microsatellite markers (Table S1) distributed across chr. 12 in parasites from the Thai-Burma border and Laos. These included a cluster of 11 markers within 14 kb of gch1. Expected heterozygosity (He) was high across chr. 12 in Laos (mean = 0.85, s.d = 0.08) and at markers situated far from gch1 in Thai parasites. However, for the 11 markers flanking gch1 variation was halved in Thai parasites (He (±s.d.) = 0.83 (±0.07) in Laos vs He = 0.41±0.16 in Thailand) (Figure 4) and variation was reduced in Thailand for 600–950 kb (40–63 cM). These data are consistent with strong recent selection acting on gch1 CNP. Comparison of this selective event with selective sweeps around known drug resistance genes provides a means to assess the strength of this selective event. We have previously described patterns of microsatellite variation around dhfr (chr. 4), the chloroquine resistance transporter (pfcrt (chr. 7) using parasites collected from the same clinic [27]. We observed significant reduction in variation for 98–137 kb (6–8 cM) around dhfr, and for 195–268 kb (11–16 cM) around pfcrt. The window of reduced variation is considerably larger around gch1, emphasizing that selection on this locus was strong and recent. Examination of extended haplotype homozygosity (EHH) also reveal striking differences in LD between parasites from Thailand and Laos. In Laos, haplotype blocks are short and EHH decays to <0.02 within 3 kb on either side of gch1. In contrast, haplotype blocks extend largely unbroken for 63 kb (4 cM) around gch1 in Thai parasites with multiple copies of each of the three predominant amplicon types bearing gch1. These data are consistent with rapid recent spread of this CNP in Thailand (Figure 5).


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)

Haplotype structure and LD decay around gch1.(a) Plots of EHH for markers flanking gch1 from Thailand and Laos. In Thailand, EHH is plotted for the three predominant amplicon types (2.2, 7.3 and 8.7 kb). EHH for chromosomes with single copies of gch1 from both countries is shown for comparison. (b) Visual representation of LD. Microsatellite data was reduced to binary form by coloring the predominant allele in black and all other alleles in white. The 33 loci typed are arranged in order across the chromosome, while samples are arranged in rows. The country of origin of each sample is shown on the left, while the amplicon type (Figure 2) is shown on the right.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000243-g005: Haplotype structure and LD decay around gch1.(a) Plots of EHH for markers flanking gch1 from Thailand and Laos. In Thailand, EHH is plotted for the three predominant amplicon types (2.2, 7.3 and 8.7 kb). EHH for chromosomes with single copies of gch1 from both countries is shown for comparison. (b) Visual representation of LD. Microsatellite data was reduced to binary form by coloring the predominant allele in black and all other alleles in white. The 33 loci typed are arranged in order across the chromosome, while samples are arranged in rows. The country of origin of each sample is shown on the left, while the amplicon type (Figure 2) is shown on the right.
Mentions: If chromosomes carrying gch1 CNP have been under strong recent selection in Thailand, we would predict that genetic diversity would be reduced and LD increased in the vicinity of gch1 on chr. 12. We measured length variation at 33 di-nucleotide microsatellite markers (Table S1) distributed across chr. 12 in parasites from the Thai-Burma border and Laos. These included a cluster of 11 markers within 14 kb of gch1. Expected heterozygosity (He) was high across chr. 12 in Laos (mean = 0.85, s.d = 0.08) and at markers situated far from gch1 in Thai parasites. However, for the 11 markers flanking gch1 variation was halved in Thai parasites (He (±s.d.) = 0.83 (±0.07) in Laos vs He = 0.41±0.16 in Thailand) (Figure 4) and variation was reduced in Thailand for 600–950 kb (40–63 cM). These data are consistent with strong recent selection acting on gch1 CNP. Comparison of this selective event with selective sweeps around known drug resistance genes provides a means to assess the strength of this selective event. We have previously described patterns of microsatellite variation around dhfr (chr. 4), the chloroquine resistance transporter (pfcrt (chr. 7) using parasites collected from the same clinic [27]. We observed significant reduction in variation for 98–137 kb (6–8 cM) around dhfr, and for 195–268 kb (11–16 cM) around pfcrt. The window of reduced variation is considerably larger around gch1, emphasizing that selection on this locus was strong and recent. Examination of extended haplotype homozygosity (EHH) also reveal striking differences in LD between parasites from Thailand and Laos. In Laos, haplotype blocks are short and EHH decays to <0.02 within 3 kb on either side of gch1. In contrast, haplotype blocks extend largely unbroken for 63 kb (4 cM) around gch1 in Thai parasites with multiple copies of each of the three predominant amplicon types bearing gch1. These data are consistent with rapid recent spread of this CNP in Thailand (Figure 5).

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