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

Handle URI:
http://hdl.handle.net/10754/325240
Title:
Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites
Authors:
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 ( 0000-0002-1755-2819 ) ; Blaxter, Mark; Cravo, Pedro
Abstract:
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)
Citation:
Hunt P, Martinelli A, Modrzynska K, Borges S, Creasey A, et al. (2010) Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics 11: 499. doi:10.1186/1471-2164-11-499.
Publisher:
Springer Nature
Journal:
BMC Genomics
Issue Date:
16-Sep-2010
DOI:
10.1186/1471-2164-11-499
PubMed ID:
20846421
PubMed Central ID:
PMC2996995
Type:
Article
ISSN:
14712164
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorHunt, Paulen
dc.contributor.authorMartinelli, Axelen
dc.contributor.authorModrzynska, Katarzynaen
dc.contributor.authorBorges, Sofiaen
dc.contributor.authorCreasey, Alisonen
dc.contributor.authorRodrigues, Louiseen
dc.contributor.authorBeraldi, Darioen
dc.contributor.authorLoewe, Laurenceen
dc.contributor.authorFawcett, Richarden
dc.contributor.authorKumar, Sujaien
dc.contributor.authorThomson, Marianen
dc.contributor.authorTrivedi, Urmien
dc.contributor.authorOtto, Thomas Den
dc.contributor.authorPain, Arnaben
dc.contributor.authorBlaxter, Marken
dc.contributor.authorCravo, Pedroen
dc.date.accessioned2014-08-27T09:41:43Z-
dc.date.available2014-08-27T09:41:43Z-
dc.date.issued2010-09-16en
dc.identifier.citationHunt P, Martinelli A, Modrzynska K, Borges S, Creasey A, et al. (2010) Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics 11: 499. doi:10.1186/1471-2164-11-499.en
dc.identifier.issn14712164en
dc.identifier.pmid20846421en
dc.identifier.doi10.1186/1471-2164-11-499en
dc.identifier.urihttp://hdl.handle.net/10754/325240en
dc.description.abstractBackground: 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.en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjectartemisininen
dc.subjectdihydrofolate reductaseen
dc.subjectproteinaseen
dc.subjectubiquitin specific proteaseen
dc.subjectunclassified drugen
dc.subjectartemisininen
dc.subjectartemisinin derivativeen
dc.subjectpyrimethamineen
dc.subjectanimal experimenten
dc.subjectanimal modelen
dc.subjectantimalarial drug resistanceen
dc.subjectchromosome 2en
dc.subjectcontrolled studyen
dc.subjectcopy number variationen
dc.subjectevolutionen
dc.subjectgene deletionen
dc.subjectgene insertionen
dc.subjectgene locusen
dc.subjectgene mappingen
dc.subjectgene mutationen
dc.subjectgenetic analysisen
dc.subjectgenetic crossen
dc.subjectgenetic markeren
dc.subjectin vivo studyen
dc.subjectlinkage analysisen
dc.subjectmalariaen
dc.subjectmissense mutationen
dc.subjectmolecular mechanicsen
dc.subjectmouseen
dc.subjectmutational analysisen
dc.subjectphenotypeen
dc.subjectPlasmodium chabaudien
dc.subjectPlasmodium falciparumen
dc.subjectpoint mutationen
dc.subjectsequence analysisen
dc.subjectcomputer simulationen
dc.subjectdirected molecular evolutionen
dc.subjectDNA sequenceen
dc.subjectdrug effecten
dc.subjectdrug resistanceen
dc.subjectgeneen
dc.subjectgene expression regulationen
dc.subjectgeneticsen
dc.subjectgenomeen
dc.subjectgenotypeen
dc.subjectindel mutationen
dc.subjectmalariaen
dc.subjectmethodologyen
dc.subjectmutationen
dc.subjectparasiteen
dc.subjectparasitologyen
dc.subjectphylogenyen
dc.subjectPlasmodium chabaudien
dc.subjectRodentiaen
dc.subjectArtemisininsen
dc.subjectComputer Simulationen
dc.subjectDirected Molecular Evolutionen
dc.subjectDNA Copy Number Variationsen
dc.subjectDrug Resistanceen
dc.subjectGenes, Protozoanen
dc.subjectGenome, Protozoanen
dc.subjectGenotypeen
dc.subjectINDEL Mutationen
dc.subjectMalariaen
dc.subjectMutagenesis, Insertionalen
dc.subjectMutationen
dc.subjectParasitesen
dc.subjectPhenotypeen
dc.subjectPhylogenyen
dc.subjectPlasmodium chabaudien
dc.subjectPoint Mutationen
dc.subjectPyrimethamineen
dc.subjectSequence Analysis, DNAen
dc.subjectSequence Deletionen
dc.titleExperimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasitesen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalBMC Genomicsen
dc.identifier.pmcidPMC2996995en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionInstitute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdomen
dc.contributor.institutionCentre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdomen
dc.contributor.institutionCentro de Malaria e Outras Doenas Tropicais/IHMT/UEI Biologia Molecular, Universidade Nova de Lisboa, Lisbon, Portugalen
dc.contributor.institutionCentro de Malaria e Outras Doenas Tropicais/IHMT/UEI Malaria, Universidade Nova de Lisboa, Lisbon, Portugalen
dc.contributor.institutionInstitute for Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdomen
dc.contributor.institutionCentre for Systems Biology at Edinburgh, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdomen
dc.contributor.institutionThe GenePool, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdomen
dc.contributor.institutionPathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdomen
dc.contributor.institutionDivision of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, United Kingdomen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorPain, Arnaben

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