A comprehensive evaluation of rodent malaria parasite genomes and gene expression

Otto, T. D. et al. (2014) A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biology, 12(1), p. 86. (doi: 10.1186/s12915-014-0086-0) (PMID:25359557) (PMCID:PMC4242472)

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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 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. falciparumand 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 Plasmodiumbiology. 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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Billker, Dr Oliver and Religa, Miss Agnieszka and Waters, Professor Andy and Otto, Dr Thomas
Authors: Otto, T. D., Böhme, U., Jackson, A. P., Hunt, M., Franke-Fayard, B., Hoeijmakers, W. A. M., Religa, A. A., Robertson, L., Sanders, M., Ogun, S. A., Cunningham, D., Erhart, A., Billker, O., Khan, S. M., Stunnenberg, H. G., Langhorne, J., Holder, A. A., Waters, A. P., Newbold, C. I., Pain, A., Berriman, M., and Janse, C. J.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:BMC Biology
Publisher:BioMed Central
ISSN:1741-7007
ISSN (Online):1741-7007
Copyright Holders:Copyright © 2014 The Authors
First Published:First published in BMC Biology 12(1):86
Publisher Policy:Reproduced under a Creative Commons License

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