the central role that erythrocyte invasion plays in Plasmodium falciparum survival and reproduction makes this process an attractive target for therapeutic or vaccine development. However, multiple invasion-related genes with complementary and overlapping functions afford the parasite the plasticity to vary ligands used for invasion, leading to phenotypic variation and immune evasion. Overcoming the challenge posed by redundant ligands requires a deeper understanding of conditions that select for variant phenotypes and the molecular mediators. While host factors including receptor heterogeneity and acquired immune responses may drive parasite phenotypic variation, we have previously shown that host-independent changes in invasion phenotype can be achieved by continuous culturing of the W2mef and Dd2 P. falciparum strains in moving suspension as opposed to static conditions. Here, we have used a highly biologically replicated whole transcriptome sequencing approach to identify the molecular signatures of variation associated with the phenotype switch. The data show increased expression of particular invasion-related genes in switched parasites, as well as a large number of genes encoding proteins that are either exported or form part of the export machinery. The genes with most markedly increased expression included members of the erythrocyte binding antigens (EBA), reticulocyte binding homologues (RH), surface associated interspersed proteins (SURFIN), exported protein family 1 (EPF1) and Plasmodium Helical Interspersed Sub-Telomeric (PHIST) gene families. the data indicate changes in expression of a repertoire of genes not previously associated with erythrocyte invasion phenotypes, suggesting the possibility that moving suspension culture may also select for other traits.Plasmodium falciparum malaria remains a major global public health challenge 1-3 . The 48-hour cyclical asexual replication of the blood stage parasite is responsible for the clinical symptoms of the infection 4 . Parasite control is hampered by genetic and phenotypic variations that impact negatively on drug and vaccine development strategies. Thus, a better understanding of the molecular mechanisms responsible for parasite phenotypic variation is important for the development and application of new malaria control strategies.Erythrocyte invasion by P. falciparum merozoites has been a subject of significant research interest due to its central role in parasite survival and transmission 5-7 . Some of these studies have demonstrated the importance of invasion-related gene families in the parasite genome, particularly the erythrocyte binding antigens (EBAs) and reticulocyte binding-like homologues (RHs) 5,8-16 . The array of different genes involved in invasion allows the parasite to vary ligands used for invasion [17][18][19][20] , enabling adaptation to differences in host environments including erythrocyte receptor heterogeneity and ligand-specific immune responses [21][22][23][24][25] . Expression and usage of particular ligands appear to depe...