Long- and short-term selective forces on malaria parasite genomes

TY - JOUR

T1 - Long- and short-term selective forces on malaria parasite genomes

AU - Nygaard, Sanne

AU - Braunstein, Alexander

AU - Malsen, Gareth

AU - Van Dongen, Stijn

AU - Gardner, Paul P

AU - Krogh, Anders

AU - Otto, Thomas D

AU - Pain, Arnab

AU - Berriman, Matthew

AU - McAuliffe, Jon

AU - Dermitzakis, Emmanouil T

AU - Jeffares, Daniel C

PY - 2010/9/1

Y1 - 2010/9/1

N2 - 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.

AB - 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.

KW - Animals

KW - Conserved Sequence

KW - Genes, Protozoan

KW - Genome, Protozoan

KW - Malaria

KW - Open Reading Frames

KW - Parasites

KW - Phylogeny

KW - Plasmodium

KW - Selection, Genetic

KW - Species Specificity

KW - Time Factors

U2 - 10.1371/journal.pgen.1001099

DO - 10.1371/journal.pgen.1001099

M3 - Journal article

C2 - 20838588

SN - 1553-7390

VL - 6

JO - P L o S Genetics

JF - P L o S Genetics

IS - 9

ER -