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Nucleic Acids Research 2006 34(4):1166-1173; doi:10.1093/nar/gkj517
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Published online 21 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains

Manuel Llinás, Zbynek Bozdech1, Edith D. Wong2, Alex T. Adai2 and Joseph L. DeRisi2,*

Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University 246 Carl Icahn Laboratory, Princeton NJ 08544, USA 1School of Biological Sciences, Nanyang Technological University 60 Nanyang Drive, Singapore 637551 2Department of Biochemistry and Biophysics, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2542, USA

*To whom correspondence should be addressed. Tel: +1 415 476 4132; Fax: +1 415 514 4140; Email: joe{at}derisilab.ucsf.edu

Received October 28, 2005. Revised December 3, 2005. Accepted January 13, 2006.

Gene expression patterns have been demonstrated to be highly variable between similar cell types, for example lab strains and wild strains of Saccharomyces cerevisiae cultured under identical growth conditions exhibit a wide range of expression differences. We have used a genome-wide approach to characterize transcriptional differences between strains of Plasmodium falciparum by characterizing the transcriptome of the 48 h intraerythrocytic developmental cycle (IDC) for two strains, 3D7 and Dd2 and compared these results to our prior work using the HB3 strain. These three strains originate from geographically diverse locations and possess distinct drug sensitivity phenotypes. Our goal was to identify transcriptional differences related to phenotypic properties of these strains including immune evasion and drug sensitivity. We find that the highly streamlined transcriptome is remarkably well conserved among all three strains, and differences in gene expression occur mainly in genes coding for surface antigens involved in parasite–host interactions. Our analysis also detects several transcripts that are unique to individual strains as well as identifying large chromosomal deletions and highly polymorphic regions across strains. The majority of these genes are uncharacterized and have no homology to other species. These tractable transcriptional differences provide important phenotypes for these otherwise highly related strains of Plasmodium.


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