Long- and Short-Term Selective Forces on Malaria Parasite Genomes

• Published in: PLoS genetics Vol. 6; no. 9; p. e1001099
• Main Authors: Nygaard, Sanne, Braunstein, Alexander, Malsen, Gareth, Van Dongen, Stijn, Gardner, Paul P., Krogh, Anders, Otto, Thomas D., Pain, Arnab, Berriman, Matthew, McAuliffe, Jon, Dermitzakis, Emmanouil T., Jeffares, Daniel C.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.09.2010; Public Library of Science (PLoS)
• Subjects: Animals; Conserved Sequence - genetics; Evolutionary Biology/Genomics; Exon (Molecular genetics); Genes, Protozoan - genetics; Genetic aspects; Genetics; Genetics and Genomics/Comparative Genomics; Genetics and Genomics/Population Genetics; Genome, Protozoan - genetics; Genomics; Identification and classification; Infectious Diseases; Malaria; Malaria - parasitology; Open Reading Frames - genetics; Parasites - genetics; Phylogeny; Plasmodium; Plasmodium - genetics; Plasmodium falciparum; Properties; Proteins; Selection, Genetic; Single nucleotide polymorphisms; Species Specificity; Time Factors; United Kingdom
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1001099

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.