Long- and short-term selective forces on malaria parasite genomes.
Plasmodium parasites, the causal agents of malaria, result in more than 1 million deaths annually. Plasmodium are unicellular eukaryotes with small ∼23 Mb genomes encoding ∼5200 protein-coding genes. The protein-coding genes comprise about half of these genomes. Although evolutionary processes have a significant impact on malaria control, the selective pressures within Plasmodium genomes are poorly understood, particularly in the non-protein-coding portion of the genome. We use evolutionary methods to describe selective processes in both the coding and non-coding regions of these genomes. Based on genome alignments of seven Plasmodium species, we show that protein-coding, intergenic and intronic regions are all subject to purifying selection and we identify 670 conserved non-genic elements. We then use genome-wide polymorphism data from P. falciparum to describe short-term selective processes in this species and identify some candidate genes for balancing (diversifying) selection. Our analyses suggest that there are many functional elements in the non-genic regions of these genomes and that adaptive evolution has occurred more frequently in the protein-coding regions of the genome.
Nygaard
Sanne
S
Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.
Braunstein
Alexander
A
Malsen
Gareth
G
Van Dongen
Stijn
S
Gardner
Paul P
PP
Krogh
Anders
A
Otto
Thomas D
TD
Pain
Arnab
A
Berriman
Matthew
M
McAuliffe
Jon
J
Dermitzakis
Emmanouil T
ET
Jeffares
Daniel C
DC
D000818:Animals; D017124:Conserved Sequence / Q000235:genetics; D017125:Genes, Protozoan / Q000235:genetics; D018503:Genome, Protozoan / Q000235:genetics*; D008288:Malaria / Q000469:parasitology*; D016366:Open Reading Frames / Q000235:genetics; D010271:Parasites / Q000235:genetics*; D010802:Phylogeny; D010961:Plasmodium / Q000235:genetics*; D012641:Selection, Genetic; D013045:Species Specificity; D013997:Time Factors