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

Handle URI:
http://hdl.handle.net/10754/325277
Title:
Long- and short-term selective forces on malaria parasite genomes
Authors:
Nygaard, Sanne; Braunstein, Alexander; Malsen, Gareth; Van Dongen, Stijn; Gardner, Paul P.; Krogh, Anders; Otto, Thomas D.; Pain, Arnab ( 0000-0002-1755-2819 ) ; Berriman, Matthew; McAuliffe, Jon; Dermitzakis, Emmanouil T.; Jeffares, Daniel C.
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.
KAUST Department:
Computational Bioscience Research Center (CBRC)
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
Journal:
PLoS Genetics
Issue Date:
9-Sep-2010
DOI:
10.1371/journal.pgen.1001099
PubMed ID:
20838588
PubMed Central ID:
PMC2936524
Type:
Article
ISSN:
15537390
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorNygaard, Sanneen
dc.contributor.authorBraunstein, Alexanderen
dc.contributor.authorMalsen, Garethen
dc.contributor.authorVan Dongen, Stijnen
dc.contributor.authorGardner, Paul P.en
dc.contributor.authorKrogh, Andersen
dc.contributor.authorOtto, Thomas D.en
dc.contributor.authorPain, Arnaben
dc.contributor.authorBerriman, Matthewen
dc.contributor.authorMcAuliffe, Jonen
dc.contributor.authorDermitzakis, Emmanouil T.en
dc.contributor.authorJeffares, Daniel C.en
dc.date.accessioned2014-08-27T09:44:28Z-
dc.date.available2014-08-27T09:44:28Z-
dc.date.issued2010-09-09en
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.en
dc.identifier.issn15537390en
dc.identifier.pmid20838588en
dc.identifier.doi10.1371/journal.pgen.1001099en
dc.identifier.urihttp://hdl.handle.net/10754/325277en
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.en
dc.language.isoenen
dc.publisherPublic Library of Scienceen
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.en
dc.rightsArchived with thanks to PLoS Geneticsen
dc.subjectcontrolled studyen
dc.subjectevolutionary adaptationen
dc.subjectgenetic associationen
dc.subjectgenetic codeen
dc.subjectgenetic conservationen
dc.subjectgenetic differenceen
dc.subjectgenetic identificationen
dc.subjectgenetic modelen
dc.subjectgenetic polymorphismen
dc.subjectgenetic selectionen
dc.subjectgenetic variabilityen
dc.subjectgenome analysisen
dc.subjecthost parasite interactionen
dc.subjectmathematical computingen
dc.subjectparasite survivalen
dc.subjectPlasmodiumen
dc.subjectPlasmodium falciparumen
dc.subjectsequence alignmenten
dc.subjectConserved Sequenceen
dc.subjectGenes, Protozoanen
dc.subjectGenome, Protozoanen
dc.subjectMalariaen
dc.subjectOpen Reading Framesen
dc.subjectParasitesen
dc.subjectPhylogenyen
dc.subjectPlasmodiumen
dc.subjectSelection, Geneticen
dc.subjectSpecies Specificityen
dc.subjectTime Factorsen
dc.subjectPlasmodium falciparumen
dc.subjectPlasmodium parasitesen
dc.subjectProtistaen
dc.titleLong- and short-term selective forces on malaria parasite genomesen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalPLoS Geneticsen
dc.identifier.pmcidPMC2936524en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionBioinformatics Centre, University of Copenhagen, Copenhagen, Denmarken
dc.contributor.institutionBiotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmarken
dc.contributor.institutionCenter for Social Evolution, University of Copenhagen, Copenhagen, Denmarken
dc.contributor.institutionStatistics Department, University of Pennsylvania, Philadelphia, PA, United Statesen
dc.contributor.institutionGoogle, Inc, Mountain View, CA, United Statesen
dc.contributor.institutionWellcome Trust Sanger Institute, Cambridge, United Kingdomen
dc.contributor.institutionRNA Genomics, European Bioinformatics Institute, Cambridge, United Kingdomen
dc.contributor.institutionDepartment of Genetic Medicine and Development, University of Geneva, Geneva, Switzerlanden
dc.contributor.institutionDepartment of Genetics, Evolution and Environment, University College London, United Kingdomen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorPain, Arnaben

Related articles on PubMed

All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.