title: Adaptive copy number evolution in malaria parasites.
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.
authors.affiliation: Southwest Foundation for Biomedical Research (SFBR), San Antonio, TX, USA.
authors.forename: Shalini
authors.initials: S
authors.lastname: Nair
authors.forename: Becky
authors.initials: B
authors.lastname: Miller
authors.forename: Marion
authors.initials: M
authors.lastname: Barends
authors.forename: Anchalee
authors.initials: A
authors.lastname: Jaidee
authors.forename: Jigar
authors.initials: J
authors.lastname: Patel
authors.forename: Mayfong
authors.initials: M
authors.lastname: Mayxay
authors.forename: Paul
authors.initials: P
authors.lastname: Newton
authors.forename: François
authors.initials: F
authors.lastname: Nosten
authors.forename: Michael T
authors.initials: MT
authors.lastname: Ferdig
authors.forename: Tim J C
authors.initials: TJ
authors.lastname: Anderson
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D000962:Antimalarials / Q000494:pharmacology / Q000627:therapeutic use; D004351:Drug Resistance; D019143:Evolution, Molecular; D005493:Folic Acid Antagonists / Q000494:pharmacology* / Q000627:therapeutic use; D006136:GTP Cyclohydrolase / Q000235:genetics* / Q000378:metabolism; D018628:Gene Dosage; D017125:Genes, Protozoan; D005843:Geography; D006801:Humans; D007812:Laos; D015810:Linkage Disequilibrium; D016778:Malaria, Falciparum / Q000188:drug therapy / Q000469:parasitology; D018895:Microsatellite Repeats; D020411:Oligonucleotide Array Sequence Analysis; D010453:Peptide Synthases / Q000235:genetics / Q000378:metabolism; D010963:Plasmodium falciparum / Q000187:drug effects / Q000201:enzymology / Q000235:genetics*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D013762:Tetrahydrofolate Dehydrogenase / Q000235:genetics / Q000378:metabolism; D013785:Thailand
chemical_list: D000962:Antimalarials; D005493:Folic Acid Antagonists; D013762:Tetrahydrofolate Dehydrogenase; D006136:GTP Cyclohydrolase; D010453:Peptide Synthases; C020041:dihydrofolate synthetase