• 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 KAUSTCommunitiesIssue DateSubmit DateThis CollectionIssue DateSubmit Date

    My Account

    Login

    Quick Links

    Open Access PolicyORCID LibguidePlumX LibguideSubmit an Item

    Statistics

    Display statistics

    Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Type
    Article
    Authors
    Assefa, Samuel
    Lim, Caeul
    Preston, Mark D.
    Duffy, Craig W.
    Nair, Mridul
    Adroub, Sabir
    Kadir, Khamisah A.
    Goldberg, Jonathan M.
    Neafsey, Daniel E.
    Divis, Paul
    Clark, Taane G. cc
    Duraisingh, Manoj T.
    Conway, David J.
    Pain, Arnab cc
    Singh, Balbir
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Computational Bioscience Research Center (CBRC)
    Date
    2015-10-05
    Online Publication Date
    2015-10-05
    Print Publication Date
    2015-10-20
    Permanent link to this record
    http://hdl.handle.net/10754/622357
    
    Metadata
    Show full item record
    Abstract
    Malaria cases caused by the zoonotic parasite Plasmodium knowlesi are being increasingly reported throughout Southeast Asia and in travelers returning from the region. To test for evidence of signatures of selection or unusual population structure in this parasite, we surveyed genome sequence diversity in 48 clinical isolates recently sampled from Malaysian Borneo and in five lines maintained in laboratory rhesus macaques after isolation in the 1960s from Peninsular Malaysia and the Philippines. Overall genomewide nucleotide diversity (π = 6.03 × 10) was much higher than has been seen in worldwide samples of either of the major endemic malaria parasite species Plasmodium falciparum and Plasmodium vivax. A remarkable substructure is revealed within P. knowlesi, consisting of two major sympatric clusters of the clinical isolates and a third cluster comprising the laboratory isolates. There was deep differentiation between the two clusters of clinical isolates [mean genomewide fixation index (F) = 0.21, with 9,293 SNPs having fixed differences of F = 1.0]. This differentiation showed marked heterogeneity across the genome, with mean F values of different chromosomes ranging from 0.08 to 0.34 and with further significant variation across regions within several chromosomes. Analysis of the largest cluster (cluster 1, 38 isolates) indicated long-term population growth, with negatively skewed allele frequency distributions (genomewide average Tajima's D = -1.35). Against this background there was evidence of balancing selection on particular genes, including the circumsporozoite protein (csp) gene, which had the top Tajima's D value (1.57), and scans of haplotype homozygosity implicate several genomic regions as being under recent positive selection.
    Citation
    Assefa S, Lim C, Preston MD, Duffy CW, Nair MB, et al. (2015) Population genomic structure and adaptation in the zoonotic malaria parasitePlasmodium knowlesi. Proceedings of the National Academy of Sciences 112: 13027–13032. Available: http://dx.doi.org/10.1073/pnas.1509534112.
    Sponsors
    We thank all patients, nurses, doctors, and laboratory technicians at Kapit and Betong Hospitals and core staff in our research institutes for their assistance; Hifzur Rahman Ansari (King Abdullah University of Science and Technology) for submission of the sequences to European Nucleotide Archive; the Malaria Research and Reference Reagent Resource Center for providing the P. knowlesi strains contributed by William E. Collins; and the Director General of Health in Malaysia for permission to publish this paper. This study was supported by Universiti Malaysia Sarawak Grants E14054/F05/54PK1/09/2012(01) and 01(TD03)/1003/2013(01); UK Medical Research Council Grants MRC G1100123, MR/K000551/1, and MR/M01360X/1; European Research Council Advanced Award AdG-2011-294428; NIH Grant 5R01AI091787; Bill and Melinda Gates Foundation Grant OPP1023594; a postgraduate scholarship from the Ministry of Education in Malaysia; and faculty baseline funding from King Abdullah University of Science and Technology.
    Publisher
    Proceedings of the National Academy of Sciences
    Journal
    Proceedings of the National Academy of Sciences
    DOI
    10.1073/pnas.1509534112
    PubMed ID
    26438871
    PubMed Central ID
    PMC4620865
    ae974a485f413a2113503eed53cd6c53
    10.1073/pnas.1509534112
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC)

    entitlement

    Related articles

    • Diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium knowlesi in Malaysia.
    • Authors: Ahmed MA, Lau YL, Quan FS
    • Issue date: 2018 Jul 27
    • Genetic Diversity, Natural Selection and Haplotype Grouping of Plasmodium knowlesi Gamma Protein Region II (PkγRII): Comparison with the Duffy Binding Protein (PkDBPαRII).
    • Authors: Fong MY, Rashdi SA, Yusof R, Lau YL
    • Issue date: 2016
    • Within-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand.
    • Authors: Ahmed MA, Chu KB, Vythilingam I, Quan FS
    • Issue date: 2018 Nov 29
    • Genetic Diversity and Natural Selection of the Plasmodium knowlesi Circumsporozoite Protein Nonrepeat Regions.
    • Authors: Fong MY, Ahmed MA, Wong SS, Lau YL, Sitam F
    • Issue date: 2015
    • Distinct genetic difference between the Duffy binding protein (PkDBPαII) of Plasmodium knowlesi clinical isolates from North Borneo and Peninsular Malaysia.
    • Authors: Fong MY, Rashdi SA, Yusof R, Lau YL
    • Issue date: 2015 Feb 21
    DSpace software copyright © 2002-2021  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.