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Public Library of Science, PLoS Genetics, 9(6), p. e1001099, 2010

DOI: 10.1371/journal.pgen.1001099

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

Journal article published in 2010 by Sanne Nygaard, Alexander Braunstein, Gareth Malsen, Stijn Van Dongen, Paul P. Gardner, Anders Krogh, Thomas D. Otto, Arnab Pain, Matthew Berriman, Jon McAuliffe, Emmanouil T. Dermitzakis, Daniel C. Jeffares ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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. © 2010 Nygaard et al.