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dc.contributor.authorOtto, Thomas D
dc.contributor.authorBöhme, Ulrike
dc.contributor.authorJackson, Andrew P
dc.contributor.authorHunt, Martin
dc.contributor.authorFranke-Fayard, Blandine
dc.contributor.authorHoeijmakers, Wieteke A M
dc.contributor.authorReliga, Agnieszka A
dc.contributor.authorRobertson, Lauren
dc.contributor.authorSanders, Mandy
dc.contributor.authorOgun, Solabomi A
dc.contributor.authorCunningham, Deirdre
dc.contributor.authorErhart, Annette
dc.contributor.authorBillker, Oliver
dc.contributor.authorKhan, Shahid M
dc.contributor.authorStunnenberg, Hendrik G
dc.contributor.authorLanghorne, Jean
dc.contributor.authorHolder, Anthony A.
dc.contributor.authorWaters, Andrew P
dc.contributor.authorNewbold, Chris I
dc.contributor.authorPain, Arnab
dc.contributor.authorBerriman, Matthew
dc.contributor.authorJanse, Chris J
dc.date.accessioned2014-11-30T13:32:45Z
dc.date.available2014-11-30T13:32:45Z
dc.date.issued2014-10-30
dc.identifier.citationA comprehensive evaluation of rodent malaria parasite genomes and gene expression 2014, 12 (1) BMC Biology
dc.identifier.issn1741-7007
dc.identifier.pmid25359557
dc.identifier.doi10.1186/s12915-014-0086-0
dc.identifier.urihttp://hdl.handle.net/10754/336369
dc.description.abstractBackground: Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function. Results: We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilized it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the `Plasmodium interspersed repeat genes' (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family. Conclusions: Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.
dc.language.isoen
dc.publisherSpringer Nature
dc.relation.urlhttp://www.biomedcentral.com/1741-7007/12/86
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.titleA comprehensive evaluation of rodent malaria parasite genomes and gene expression
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentPathogen Genomics Laboratory
dc.identifier.journalBMC Biology
dc.identifier.pmcidPMC4242472
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionWellcome Trust Sanger Institute, Hinxton, Cambridge, UK
dc.contributor.institutionDepartment of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
dc.contributor.institutionLeiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
dc.contributor.institutionDepartment of Molecular Biology, Science faculty, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
dc.contributor.institutionInstitute of Infection, Immunity & Inflammation, School of Medical, Veterinary & Life Sciences, & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, Scotland, UK
dc.contributor.institutionDivision of Parasitology, MRC National Institute for Medical Research, Mill Hill, London, UK
dc.contributor.institutionUnit of Malariology, Institute of Tropical Medicine, Antwerp, Belgium
dc.contributor.institutionWeatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
dc.contributor.institutionWeatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personPain, Arnab
refterms.dateFOA2018-06-13T15:32:23Z
dc.date.published-online2014-10-30
dc.date.published-print2014-12


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