Chromosome-level genome assemblies of three human Plasmodium species obtained directly from natural infections

This study presents high-quality, chromosome-level reference genomes for Plasmodium ovale wallikeri, Plasmodium malariae and Plasmodium falciparum sampled directly from natural infections. Using PacBio Ultra-Low Input HiFi long-read sequencing directly on enriched parasites from clinical samples collected in Mali, the challenges of low parasite biomass and the lack of in vitro culture systems for these species were overcome. The resulting assemblies resolve previously inaccessible subtelomeric regions and lead to increased gene annotations and structural insights. These resources lay the groundwork for better diagnostics, therapeutic target discovery, and comparative evolutionary studies of malaria parasites. The genomic data and the underlying approach to generate these genomes are valuable resources for the malaria community.