Plasmodium falciparum RNA, from sorted infected primary human hepatocytes, was extracted using the miRNeasy Micro Kit (QIAGEN) according to the manufacturer's instructions, including on-column DNase digestion. Plasmodium vivax RNA was extracted using TRIzol (Thermo Fisher) and purified using RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. RNA libraries for plasmodium falciparum RNA-seq were prepared using SMART-seq v4 Ultra Low Input (Clontech). RNA libraries for plasmodium vivax RNA-seq were prepared according to the SureSelect XT RNA Target Enrichment for Illumina Multiplexed Sequencing protocol from Agilent.