title: Long- and short-term selective forces on malaria parasite genomes.
abstract: 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.
authors.affiliation: Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Sanne
authors.initials: S
authors.lastname: Nygaard
authors.forename: Alexander
authors.initials: A
authors.lastname: Braunstein
authors.forename: Gareth
authors.initials: G
authors.lastname: Malsen
authors.forename: Stijn
authors.initials: S
authors.lastname: Van Dongen
authors.forename: Paul P
authors.initials: PP
authors.lastname: Gardner
authors.forename: Anders
authors.initials: A
authors.lastname: Krogh
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Otto
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
authors.forename: Jon
authors.initials: J
authors.lastname: McAuliffe
authors.forename: Emmanouil T
authors.initials: ET
authors.lastname: Dermitzakis
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Jeffares
mesh_terms: 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