• Login
    View Item 
    •   Home
    • Research
    • Articles
    • View Item
    •   Home
    • Research
    • Articles
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of KAUSTCommunitiesTitleAuthorsKAUST AuthorsIssue DateSubmit DateSubjectsThis CollectionTitleAuthorsKAUST AuthorsIssue DateSubmit DateSubjects

    My Account

    Login

    Quick Links

    Open Access PolicyORCID LibguidePlumX LibguideSubmit an Item

    Statistics

    Display statistics

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

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Thumbnail
    Name:
    Article-PLoS_Genet-Long-_and_- ...
    Size:
    739.2Kb
    Format:
    PDF
    Description:
    Article - Full Text
    Download
    Thumbnail
    Name:
    Supplement_1_-_PLoS_Genet-Long ...
    Size:
    120.5Kb
    Format:
    PDF
    Description:
    Supplemental File 1
    Download
    Thumbnail
    Name:
    Supplement_2_-_PLoS_Genet-Long ...
    Size:
    114.0Kb
    Format:
    PDF
    Description:
    Supplemental File 2
    Download
    Thumbnail
    Name:
    Supplement_3_-_PLoS_Genet-Long ...
    Size:
    39.09Kb
    Format:
    PDF
    Description:
    Supplemental File 3
    Download
    Thumbnail
    Name:
    Supplement_4_-_PLoS_Genet-Long ...
    Size:
    97.76Kb
    Format:
    PDF
    Description:
    Supplemental File 4
    Download
    Thumbnail
    Name:
    Supplement_5_-_PLoS_Genet-Long ...
    Size:
    32.57Kb
    Format:
    PDF
    Description:
    Supplemental File 5
    Download
    Thumbnail
    Name:
    Supplement_6_-_PLoS_Genet-Long ...
    Size:
    173Kb
    Format:
    Microsoft Word
    Description:
    Supplemental File 6
    Download
    Thumbnail
    Name:
    Supplement_7_-_PLoS_Genet-Long ...
    Size:
    51Kb
    Format:
    Microsoft Word
    Description:
    Supplemental File 7
    Download
    Thumbnail
    Name:
    Supplement_8_-_PLoS_Genet-Long ...
    Size:
    39.5Kb
    Format:
    Microsoft Word
    Description:
    Supplemental File 8
    Download
    Thumbnail
    Name:
    Supplement_9_-_PLoS_Genet-Long ...
    Size:
    40Kb
    Format:
    Microsoft Word
    Description:
    Supplemental File 9
    Download
    Thumbnail
    Name:
    Supplement_10_-_PLoS_Genet-Lon ...
    Size:
    87Kb
    Format:
    Microsoft Word
    Description:
    Supplemental File 10
    Download
    Thumbnail
    Name:
    Supplement_11_-_PLoS_Genet-Lon ...
    Size:
    44Kb
    Format:
    Microsoft Word
    Description:
    Supplemental File 11
    Download
    Thumbnail
    Name:
    Supplement_12_-_PLoS_Genet-Lon ...
    Size:
    56Kb
    Format:
    Microsoft Word
    Description:
    Supplemental File 12
    Download
    Thumbnail
    Name:
    Supplement_13_-_PLoS_Genet-Lon ...
    Size:
    46.5Kb
    Format:
    Microsoft Word
    Description:
    Supplemental File 13
    Download
    Thumbnail
    Name:
    Supplement_14_-_PLoS_Genet-Lon ...
    Size:
    399Kb
    Format:
    Microsoft Word
    Description:
    Supplemental File 14
    Download
    View more filesView fewer files
    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
    Computational Bioscience Research Center (CBRC)
    Date
    2010-09-09
    Permanent link to this record
    http://hdl.handle.net/10754/325277
    
    Metadata
    Show full item record
    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
    ISSN
    15537390
    DOI
    10.1371/journal.pgen.1001099
    PubMed ID
    20838588
    PubMed Central ID
    PMC2936524
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pgen.1001099
    Scopus Count
    Collections
    Articles; Computational Bioscience Research Center (CBRC)

    entitlement

    Related articles

    • An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome.
    • Authors: Durand PM, Oelofse AJ, Coetzer TL
    • Issue date: 2006 Nov 4
    • Divergent evolutionary constraints on mitochondrial and nuclear genomes of malaria parasites.
    • Authors: McIntosh MT, Srivastava R, Vaidya AB
    • Issue date: 1998 Sep 1
    • Molecular systematics of the three mitochondrial protein-coding genes of malaria parasites: corroborative and new evidence for the origins of human malaria.
    • Authors: Perkins SL
    • Issue date: 2008 Dec
    • Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents.
    • Authors: Prugnolle F, McGee K, Keebler J, Awadalla P
    • Issue date: 2008 Jul 30
    • Divergence of the mitochondrial genome structure in the apicomplexan parasites, Babesia and Theileria.
    • Authors: Hikosaka K, Watanabe Y, Tsuji N, Kita K, Kishine H, Arisue N, Palacpac NM, Kawazu S, Sawai H, Horii T, Igarashi I, Tanabe K
    • Issue date: 2010 May

    Related items

    Showing items related by title, author, creator and subject.

    • Thumbnail

      Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS)

      Lawton, Jennifer; Brugat, Thibaut; Yan, Yam Xue; Reid, Adam James; Böhme, Ulrike; Otto, Thomas Dan; Pain, Arnab; Jackson, Andrew; Berriman, Matthew; Cunningham, Deirdre; Preiser, Peter; Langhorne, Jean (Springer Nature, 2012-03-29)
      Background: The pir genes comprise the largest multi-gene family in Plasmodium, with members found in P. vivax, P. knowlesi and the rodent malaria species. Despite comprising up to 5% of the genome, little is known about the functions of the proteins encoded by pir genes. P. chabaudi causes chronic infection in mice, which may be due to antigenic variation. In this model, pir genes are called cirs and may be involved in this mechanism, allowing evasion of host immune responses. In order to fully understand the role(s) of CIR proteins during P. chabaudi infection, a detailed characterization of the cir gene family was required.Results: The cir repertoire was annotated and a detailed bioinformatic characterization of the encoded CIR proteins was performed. Two major sub-families were identified, which have been named A and B. Members of each sub-family displayed different amino acid motifs, and were thus predicted to have undergone functional divergence. In addition, the expression of the entire cir repertoire was analyzed via RNA sequencing and microarray. Up to 40% of the cir gene repertoire was expressed in the parasite population during infection, and dominant cir transcripts could be identified. In addition, some differences were observed in the pattern of expression between the cir subgroups at the peak of P. chabaudi infection. Finally, specific cir genes were expressed at different time points during asexual blood stages.Conclusions: In conclusion, the large number of cir genes and their expression throughout the intraerythrocytic cycle of development indicates that CIR proteins are likely to be important for parasite survival. In particular, the detection of dominant cir transcripts at the peak of P. chabaudi infection supports the idea that CIR proteins are expressed, and could perform important functions in the biology of this parasite. Further application of the methodologies described here may allow the elucidation of CIR sub-family A and B protein functions, including their contribution to antigenic variation and immune evasion. 2012 Lawton et al; licensee BioMed Central Ltd.
    • Thumbnail

      Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

      Hunt, Paul; Martinelli, Axel; Modrzynska, Katarzyna; Borges, Sofia; Creasey, Alison; Rodrigues, Louise; Beraldi, Dario; Loewe, Laurence; Fawcett, Richard; Kumar, Sujai; Thomson, Marian; Trivedi, Urmi; Otto, Thomas D; Pain, Arnab; Blaxter, Mark; Cravo, Pedro (Springer Nature, 2010-09-16)
      Background: Classical and quantitative linkage analyses of genetic crosses have traditionally been used to map genes of interest, such as those conferring chloroquine or quinine resistance in malaria parasites. Next-generation sequencing technologies now present the possibility of determining genome-wide genetic variation at single base-pair resolution. Here, we combine in vivo experimental evolution, a rapid genetic strategy and whole genome re-sequencing to identify the precise genetic basis of artemisinin resistance in a lineage of the rodent malaria parasite, Plasmodium chabaudi. Such genetic markers will further the investigation of resistance and its control in natural infections of the human malaria, P. falciparum.Results: A lineage of isogenic in vivo drug-selected mutant P. chabaudi parasites was investigated. By measuring the artemisinin responses of these clones, the appearance of an in vivo artemisinin resistance phenotype within the lineage was defined. The underlying genetic locus was mapped to a region of chromosome 2 by Linkage Group Selection in two different genetic crosses. Whole-genome deep coverage short-read re-sequencing (IlluminaSolexa) defined the point mutations, insertions, deletions and copy-number variations arising in the lineage. Eight point mutations arise within the mutant lineage, only one of which appears on chromosome 2. This missense mutation arises contemporaneously with artemisinin resistance and maps to a gene encoding a de-ubiquitinating enzyme.Conclusions: This integrated approach facilitates the rapid identification of mutations conferring selectable phenotypes, without prior knowledge of biological and molecular mechanisms. For malaria, this model can identify candidate genes before resistant parasites are commonly observed in natural human malaria populations. 2010 Hunt et al; licensee BioMed Central Ltd.
    • Thumbnail

      Translational repression of the cpw-wpc gene family in the malaria parasite Plasmodium

      Rao, Pavitra N.; Santos, Jorge M.; Pain, Arnab; Templeton, Thomas J.; Mair, Gunnar R. (Elsevier BV, 2016-06-14)
      The technical challenges of working with the sexual stages of the malaria parasite Plasmodium have hindered the characterization of sexual stage antigens in the quest for a successful malaria transmission-blocking vaccine. One such predicted and largely uncharacterized group of sexual stage candidate antigens is the CPW-WPC family of proteins. CPW-WPC proteins are named for a characteristic domain that contains two conserved motifs, CPxxW and WPC. Conserved across Apicomplexa, this family is also present earlier in the Alveolata in the free-living, non-parasitophorous, photosynthetic chromerids, Chromera and Vitrella. In P. falciparum and P. berghei blood stage parasites the transcripts of all nine cpw-wpc genes have been detected in gametocytes. RNA immunoprecipitation followed by reverse transcriptase-PCR reveals all P. berghei cpw-wpc transcripts to be bound by the translational repressors DOZI and CITH, and thus are likely under translational control prior to transmission from the rodent host to the mosquito vector in P. berghei. The GFP tagging of two endogenous P. berghei genes confirmed translational silencing in the gametocyte and translation in ookinetes. Establishing a luciferase transgene assay we show that the 3′ untranslated region of PF3D7_1331400 controls protein expression of this reporter in P. falciparum gametocytes. Our analyses suggest that cpw-wpc genes are translationally silenced in gametocytes across Plasmodium spp. and activated during ookinete formation and thus may have a role in transmission to the mosquito.
    DSpace software copyright © 2002-2019  DuraSpace
    Quick Guide | Contact Us | Send Feedback
    Open Repository is a service hosted by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. For anonymous users the allowed maximum amount is 50 search results.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.