Plasmodium falciparum is the causative agent of the most burdensome form of 
human malaria, affecting 200-300 million individuals per year worldwide. The 
recently sequenced genome of P. falciparum revealed over 5,400 genes, of which 
60% encode proteins of unknown function. Insights into the biochemical function 
and regulation of these genes will provide the foundation for future drug and 
vaccine development efforts toward eradication of this disease. By analyzing the 
complete asexual intraerythrocytic developmental cycle (IDC) transcriptome of 
the HB3 strain of P. falciparum, we demonstrate that at least 60% of the genome 
is transcriptionally active during this stage. Our data demonstrate that this 
parasite has evolved an extremely specialized mode of transcriptional regulation 
that produces a continuous cascade of gene expression, beginning with genes 
corresponding to general cellular processes, such as protein synthesis, and 
ending with Plasmodium-specific functionalities, such as genes involved in 
erythrocyte invasion. The data reveal that genes contiguous along the 
chromosomes are rarely coregulated, while transcription from the plastid genome 
is highly coregulated and likely polycistronic. Comparative genomic 
hybridization between HB3 and the reference genome strain (3D7) was used to 
distinguish between genes not expressed during the IDC and genes not detected 
because of possible sequence variations. Genomic differences between these 
strains were found almost exclusively in the highly antigenic subtelomeric 
regions of chromosomes. The simple cascade of gene regulation that directs the 
asexual development of P. falciparum is unprecedented in eukaryotic biology. The 
transcriptome of the IDC resembles a "just-in-time" manufacturing process 
whereby induction of any given gene occurs once per cycle and only at a time 
when it is required. These data provide to our knowledge the first comprehensive 
view of the timing of transcription throughout the intraerythrocytic development 
of P. falciparum and provide a resource for the identification of new 
chemotherapeutic and vaccine candidates.