A comprehensive evaluation of rodent malaria parasite genomes and gene expression

Handle URI:
http://hdl.handle.net/10754/336369
Title:
A comprehensive evaluation of rodent malaria parasite genomes and gene expression
Authors:
Otto, Thomas D; Böhme, Ulrike; Jackson, Andrew P; Hunt, Martin; Franke-Fayard, Blandine; Hoeijmakers, Wieteke A M; Religa, Agnieszka A; Robertson, Lauren; Sanders, Mandy; Ogun, Solabomi A; Cunningham, Deirdre; Erhart, Annette; Billker, Oliver; Khan, Shahid M; Stunnenberg, Hendrik G; Langhorne, Jean; Holder, Anthony A; Waters, Andrew P; Newbold, Chris I; Pain, Arnab ( 0000-0002-1755-2819 ) ; Berriman, Matthew; Janse, Chris J
Abstract:
Background: 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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
A comprehensive evaluation of rodent malaria parasite genomes and gene expression 2014, 12 (1) BMC Biology
Publisher:
Springer Nature
Journal:
BMC Biology
Issue Date:
30-Oct-2014
DOI:
10.1186/s12915-014-0086-0
PubMed ID:
25359557
PubMed Central ID:
PMC4242472
Type:
Article
ISSN:
1741-7007
Additional Links:
http://www.biomedcentral.com/1741-7007/12/86
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorOtto, Thomas Den
dc.contributor.authorBöhme, Ulrikeen
dc.contributor.authorJackson, Andrew Pen
dc.contributor.authorHunt, Martinen
dc.contributor.authorFranke-Fayard, Blandineen
dc.contributor.authorHoeijmakers, Wieteke A Men
dc.contributor.authorReliga, Agnieszka Aen
dc.contributor.authorRobertson, Laurenen
dc.contributor.authorSanders, Mandyen
dc.contributor.authorOgun, Solabomi Aen
dc.contributor.authorCunningham, Deirdreen
dc.contributor.authorErhart, Annetteen
dc.contributor.authorBillker, Oliveren
dc.contributor.authorKhan, Shahid Men
dc.contributor.authorStunnenberg, Hendrik Gen
dc.contributor.authorLanghorne, Jeanen
dc.contributor.authorHolder, Anthony Aen
dc.contributor.authorWaters, Andrew Pen
dc.contributor.authorNewbold, Chris Ien
dc.contributor.authorPain, Arnaben
dc.contributor.authorBerriman, Matthewen
dc.contributor.authorJanse, Chris Jen
dc.date.accessioned2014-11-30T13:32:45Z-
dc.date.available2014-11-30T13:32:45Z-
dc.date.issued2014-10-30en
dc.identifier.citationA comprehensive evaluation of rodent malaria parasite genomes and gene expression 2014, 12 (1) BMC Biologyen
dc.identifier.issn1741-7007en
dc.identifier.pmid25359557en
dc.identifier.doi10.1186/s12915-014-0086-0en
dc.identifier.urihttp://hdl.handle.net/10754/336369en
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.en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.biomedcentral.com/1741-7007/12/86en
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.en
dc.titleA comprehensive evaluation of rodent malaria parasite genomes and gene expressionen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalBMC Biologyen
dc.identifier.pmcidPMC4242472en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionWellcome Trust Sanger Institute, Hinxton, Cambridge, UKen
dc.contributor.institutionDepartment of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UKen
dc.contributor.institutionLeiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlandsen
dc.contributor.institutionDepartment of Molecular Biology, Science faculty, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlandsen
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, UKen
dc.contributor.institutionDivision of Parasitology, MRC National Institute for Medical Research, Mill Hill, London, UKen
dc.contributor.institutionUnit of Malariology, Institute of Tropical Medicine, Antwerp, Belgiumen
dc.contributor.institutionWeatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UKen
dc.contributor.institutionWeatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UKen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorPain, Arnaben

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