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dc.contributor.authorNygaard, Sanne
dc.contributor.authorBraunstein, Alexander
dc.contributor.authorMalsen, Gareth
dc.contributor.authorVan Dongen, Stijn
dc.contributor.authorGardner, Paul P.
dc.contributor.authorKrogh, Anders
dc.contributor.authorOtto, Thomas D.
dc.contributor.authorPain, Arnab
dc.contributor.authorBerriman, Matthew
dc.contributor.authorMcAuliffe, Jon
dc.contributor.authorDermitzakis, Emmanouil T.
dc.contributor.authorJeffares, Daniel C.
dc.date.accessioned2014-08-27T09:44:28Z
dc.date.available2014-08-27T09:44:28Z
dc.date.issued2010-09-09
dc.identifier.citationNygaard 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.
dc.identifier.issn15537390
dc.identifier.pmid20838588
dc.identifier.doi10.1371/journal.pgen.1001099
dc.identifier.urihttp://hdl.handle.net/10754/325277
dc.description.abstractPlasmodium 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.
dc.language.isoen
dc.publisherPublic Library of Science (PLoS)
dc.rightsNygaard et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rightsArchived with thanks to PLoS Genetics
dc.subjectcontrolled study
dc.subjectevolutionary adaptation
dc.subjectgenetic association
dc.subjectgenetic code
dc.subjectgenetic conservation
dc.subjectgenetic difference
dc.subjectgenetic identification
dc.subjectgenetic model
dc.subjectgenetic polymorphism
dc.subjectgenetic selection
dc.subjectgenetic variability
dc.subjectgenome analysis
dc.subjecthost parasite interaction
dc.subjectmathematical computing
dc.subjectparasite survival
dc.subjectPlasmodium
dc.subjectPlasmodium falciparum
dc.subjectsequence alignment
dc.subjectConserved Sequence
dc.subjectGenes, Protozoan
dc.subjectGenome, Protozoan
dc.subjectMalaria
dc.subjectOpen Reading Frames
dc.subjectParasites
dc.subjectPhylogeny
dc.subjectPlasmodium
dc.subjectSelection, Genetic
dc.subjectSpecies Specificity
dc.subjectTime Factors
dc.subjectPlasmodium falciparum
dc.subjectPlasmodium parasites
dc.subjectProtista
dc.titleLong- and short-term selective forces on malaria parasite genomes
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentPathogen Genomics Laboratory
dc.identifier.journalPLoS Genetics
dc.identifier.pmcidPMC2936524
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionBioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
dc.contributor.institutionBiotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
dc.contributor.institutionCenter for Social Evolution, University of Copenhagen, Copenhagen, Denmark
dc.contributor.institutionStatistics Department, University of Pennsylvania, Philadelphia, PA, United States
dc.contributor.institutionGoogle, Inc, Mountain View, CA, United States
dc.contributor.institutionWellcome Trust Sanger Institute, Cambridge, United Kingdom
dc.contributor.institutionRNA Genomics, European Bioinformatics Institute, Cambridge, United Kingdom
dc.contributor.institutionDepartment of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
dc.contributor.institutionDepartment of Genetics, Evolution and Environment, University College London, United Kingdom
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personPain, Arnab
refterms.dateFOA2018-06-14T03:33:02Z


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