New insights into the blood-stage transcriptome of Plasmodium falciparumusing RNA-Seq

Otto, T. D. et al. (2010) New insights into the blood-stage transcriptome of Plasmodium falciparumusing RNA-Seq. Molecular Microbiology, 76(1), pp. 12-24. (doi: 10.1111/j.1365-2958.2009.07026.x) (PMID:20141604) (PMCID:PMC2859250)

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Abstract

Recent advances in high-throughput sequencing present a new opportunity to deeply probe an organism's transcriptome. In this study, we used Illumina-based massively parallel sequencing to gain new insight into the transcriptome (RNA-Seq) of the human malaria parasite, Plasmodium falciparum. Using data collected at seven time points during the intraerythrocytic developmental cycle, we (i) detect novel gene transcripts; (ii) correct hundreds of gene models; (iii) propose alternative splicing events; and (iv) predict 5′ and 3′ untranslated regions. Approximately 70% of the unique sequencing reads map to previously annotated protein-coding genes. The RNA-Seq results greatly improve existing annotation of the P. falciparum genome with over 10% of gene models modified. Our data confirm 75% of predicted splice sites and identify 202 new splice sites, including 84 previously uncharacterized alternative splicing events. We also discovered 107 novel transcripts and expression of 38 pseudogenes, with many demonstrating differential expression across the developmental time series. Our RNA-Seq results correlate well with DNA microarray analysis performed in parallel on the same samples, and provide improved resolution over the microarray-based method. These data reveal new features of the P. falciparum transcriptional landscape and significantly advance our understanding of the parasite's red blood cell-stage transcriptome.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Otto, T. D., Wilinski, D., Assefa, S., Keane, T. M., Sarry, L. R., Böhme, U., Lemieux, J., Barrell, B., Pain, A., Berriman, M., Newbold, C., and Llinás, M.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Molecular Microbiology
Publisher:Wiley
ISSN:0950-382X
ISSN (Online):1365-2958
Published Online:04 February 2010
Copyright Holders:Copyright ©2010 The Authors
First Published:First published in Molecular Microbiology 76(1):12-24
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher

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