Fig. 3

Gene transcript levels among preparations of schizont-enriched P. falciparum cultures of laboratory-adapted clones and clinical isolates. Plots of normalised RNA-seq read counts for eight of the genes showing differences between four long-term laboratory-adapted clones (3D7, D10, Dd2 and HB3) and six recently culture-established Ghanaian clinical isolates (271, 278, 280, 286, 293 and 296). Each point shows the value for an independent biological replicate sample. For all genes, a wide variation in transcript levels among biological replicates may be noted. a The two panels show examples of genes for which one of the laboratory-adapted clones had a deletion, D10 which is missing the PF3D7_0935700 gene as part of a deleted region near the end of chromosome 9, and HB3 which is missing gene PF3D7_1371600 that encodes erythrocyte binding-like protein 1. These, and other genes with suspected or known deletions in the sampled parasites, are excluded from the list of differentially expressed genes in Table 1 but are listed Additional file 4: Table S2. b The six panels show examples of genes listed in Table 1 that are in the top quartile of expression and show a log₂ fold difference > 2 between the groups. Most of these genes have lower transcript levels in the clinical isolates (including AP2 transcription factor gene PF3D7_0420300, as well as predicted methyltransferase genes PF3D7_0422900 and PF3D7_0522300, and ubiquitin-binding protein 1 gene PF3D7_0104300). In contrast, the mspdbl2 gene PF3D7_1036300 shown in the bottom right panel had higher transcript levels in clinical isolates