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

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    Type
    Article
    Authors
    Nygaard, Sanne
    Braunstein, Alexander
    Malsen, Gareth
    Van Dongen, Stijn
    Gardner, Paul P.
    Krogh, Anders
    Otto, Thomas D.
    Pain, Arnab cc
    Berriman, Matthew
    McAuliffe, Jon
    Dermitzakis, Emmanouil T.
    Jeffares, Daniel C.
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Computational Bioscience Research Center (CBRC)
    Pathogen Genomics Laboratory
    Date
    2010-09-09
    Permanent link to this record
    http://hdl.handle.net/10754/325277
    
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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.
    Citation
    Nygaard S, Braunstein A, Malsen G, Van Dongen S, Gardner PP, et al. (2010) Long- and Short-Term Selective Forces on Malaria Parasite Genomes. PLoS Genet 6: e1001099. doi:10.1371/journal.pgen.1001099.
    Publisher
    Public Library of Science (PLoS)
    Journal
    PLoS Genetics
    DOI
    10.1371/journal.pgen.1001099
    PubMed ID
    20838588
    PubMed Central ID
    PMC2936524
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pgen.1001099
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC)

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