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Background  Control of malaria is threatened by emerging parasite resistance to artemisinin and derivative drug (ART) therapies. The molecular detail of how  Plasmodium  malaria parasites respond to ART and how this could contribute to resistance are not well understood. To address this question, we performed a transcriptomic study of dihydroartemisinin (DHA) response in  P. falciparum  K1 strain and in  P. berghei  ANKA strain using microarray and RNA-seq technology.    Results  Microarray data from DHA-treated  P. falciparum  trophozoite stage parasites revealed a response pattern that is overall less trophozoite-like and more like the other stages of asexual development. A meta-analysis of these data with previously published data from other ART treatments revealed a set of common differentially expressed genes. Notably, ribosomal protein genes are down-regulated in response to ART. A similar pattern of trophozoite transcriptomic change was observed from RNA-seq data. RNA-seq data from DHA-treated  P. falciparum  rings reveal a more muted response, although there is considerable overlap of differentially expressed genes with DHA-treated trophozoites. No genes are differentially expressed in DHA-treated  P. falciparum  schizonts. The transcriptional response of  P. berghei  to DHA treatment  in vivo  in infected mice is similar to the  P. falciparum in vitro  culture ring and trophozoite responses, in which ribosomal protein genes are notably down-regulated.    Conclusions  Ring and trophozoite stage  Plasmodium  respond to ART by arresting metabolic processes such as protein synthesis and glycolysis. This response can be protective in rings, as shown by the phenomenon of dormancy. In contrast, this response is not as protective in trophozoites owing to their commitment to a highly active and vulnerable metabolic state. The lower metabolic demands of schizonts could explain why they are less sensitive and unresponsive to ART. The ART response pattern is revealed clearly from RNA-seq data, suggesting that this technology is of great utility for studying drug response in  Plasmodium .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2040-0) contains supplementary material, which is available to authorized users.

bmc genomics

Plasmodium parasites mount an arrest response to dihydroartemisinin, as revealed by whole transcriptome shotgun sequencing (RNA-seq) and microarray study