1166–1173 Nucleic Acids Research, 2006, Vol. 34, No. 4 doi:10.1093/nar/gkj517 Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains Manuel Llina´ s, Zbynek Bozdech 1 , Edith D. Wong 2 , 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 and 2Department of Biochemistry and Biophysics, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94143-2542, USA Received October 28, 2005; Revised December 3, 2005; Accepted January 13, 2006 ABSTRACT 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 differ- ences in gene expression occur mainly in genes cod- ing for surface antigens involved in parasite–host interactions. Our analysis also detects several tran- scripts 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 homo- logy to other species. These tractable transcriptional differences provide important phenotypes for these otherwise highly related strains of Plasmodium. INTRODUCTION Malaria is one of the most prevalent afﬂictions of human- kind, affecting upwards of half a billion people and killing over 1.5 million persons annually. This disease is caused by the Plasmodium parasite, of which Plasmodium falciparum is the deadliest species. The lifecycle of P.falciparum is comprised of three major developmental stages, the mosquito, liver and intraerythrocytic stages. Upon red blood cell invasion, the parasite undergoes a complex series of morphological transitions over the next 48 h, ultimately resulting in a new population of mature merozoites, which reinitiate the intraerythrocytic developmental cycle (IDC). While there have been major global efforts to eliminate this disease over the past several decades, it continues to per- sist as a major health burden, especially to the poorest of nations (1). Malaria continues to be a major worldwide health issue because resistant strains of P.falciparum have evolved against virtually every known anti-malarial drug (2). However, the underlying mechanisms of Plasmodium drug resistance remain poorly understood. In part, resistance is due to poly- morphisms in a variety of genes including the plasmodium chloroquine resistance transporter—Pfcrt (chloroquine resist- ance) (3), dihydrofolate reductase (pyrimethamine) (4), dihydropteroate synthase (sulfa drugs) (4) and cytochrome b (atovaquone) (5). However, these polymorphisms are not sufﬁcient to completely describe drug resistance in P.fal- ciparum, because often their effects vary with strain genotype and drug concentration (6). Thus, while polymorphisms can confer drug resistance, different strains of P.falciparum may also rely on alternative mechanisms of gene regulation to overcome the selective pressures of anti-malarial drugs. These mechanisms may include overexpression of transporters in response to drug exposure, induction of alternative path- ways to bypass the effect of the compounds or repression of genes that exacerbate deleterious effects of the drug. For example, recent data suggests that meﬂoquine resistance are directly modulated by an increased copy number of the Plasmodium multi-drug resistance gene pfmdr1, resulting in an ampliﬁcation in the number of cellular transcripts produced (7). Therefore, regulatory responses in P.falciparum may act *To whom correspondence should be addressed. Tel: +1 415 476 4132; Fax: +1 415 514 4140; Email: joe@derisilab.ucsf.edu 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@oxfordjournals.org