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Background  The clinical symptoms of malaria are caused by the asexual replication of  Plasmodium  parasites in the blood of the vertebrate host. To spread to new hosts, however, the malaria parasite must differentiate into sexual forms, termed gametocytes, which are ingested by a mosquito vector. Sexual differentiation produces either female or male gametocytes, and involves significant morphological and biochemical changes. These transformations prepare gametocytes for the rapid progression to gamete formation and fertilisation, which occur within 20 min of ingestion. Here we present the transcriptomes of asexual, female, and male gametocytes in  P. berghei , and a comprehensive statistically-based differential-expression analysis of the transcriptional changes that underpin this sexual differentiation.    Results  RNA-seq analysis revealed numerous differences in the transcriptomes of female and male gametocytes compared to asexual stages. Overall, there is net downregulation of transcripts in gametocytes compared to asexual stages, with this trend more marked in female gametocytes. Our analysis identified transcriptional changes in previously-characterised gametocyte-specific pathways, which validated our approach. We also detected many previously-unreported female- and male-specific pathways and genes. Transcriptional biases in stage and gender were then used to investigate sex-specificity and sexual dimorphism of  Plasmodium  in an evolutionary context. Sex-related gene expression is well conserved between  Plasmodium  species, but relatively poorly conserved in related organisms outside this genus. This pattern of conservation is most evident in genes necessary for both male and female gametocyte formation. However, this trend is less pronounced for male-specific genes, which are more highly conserved outside the genus than genes specific to female development.    Conclusions  We characterised the transcriptional changes that are integral to the development of the female and male sexual forms of  Plasmodium . These differential-expression patterns provide a vital insight into understanding the gender-specific characteristics of this essential stage that is the primary target for treatments that block parasite transmission. Our results also offer insight into the evolution of sex genes through Alveolata, and suggest that many  Plasmodium  sex genes evolved within the genus. We further hypothesise that male gametocytes co-opted pre-existing cellular machinery in their evolutionary history, whereas female gametocytes evolved more through the development of novel, parasite-specific pathways.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-4100-0) contains supplementary material, which is available to authorized users.

Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates