A comprehensive evaluation of rodent malaria parasite genomes and gene expression

BMC Biology

Research Article

Arnab Pain¹  Andrew P Jackson²  Hendrik G Stunnenberg³  Wieteke A M Hoeijmakers³  Deirdre Cunningham⁴  Anthony A Holder⁴  Jean Langhorne⁴  Solabomi A Ogun⁴  Agnieszka A Religa⁵  Andrew P Waters⁵  Blandine Franke-Fayard⁶  Shahid M Khan⁶  Chris J Janse⁶  Annette Erhart⁷  Chris I Newbold⁸  Ulrike Böhme⁹  Matthew Berriman⁹  Thomas D Otto⁹  Martin Hunt⁹  Lauren Robertson⁹  Mandy Sanders⁹  Oliver Billker⁹ 

[1] Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia;Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK;Department of Molecular Biology, Science faculty, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands;Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London, UK;Institute 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;Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands;Unit of Malariology, Institute of Tropical Medicine, Antwerp, Belgium;Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK;Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK;Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK;

关键词: Plasmodium chabaudi;    Plasmodium berghei;    Plasmodium yoelii;    Genomes;    RNA-seq;    Genotypic diversity;    Multigene families;    pirs;    Phylogeny;   

DOI  :  10.1186/s12915-014-0086-0

 received in 2014-07-28, accepted in 2014-10-10,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundRodent 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.ResultsWe 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 utilised 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.ConclusionsComplete 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.

【 授权许可】

Unknown   
© Otto et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This 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.