New reference genomes to distinguish the sympatric malaria parasites, Plasmodium ovale curtisi and Plasmodium ovale wallikeri

Abstract

Despite Plasmodium ovale curtisi (Poc) and wallikeri (Pow) being important human-infecting malaria parasites that are widespread across Africa and Asia, little is known about their genome diversity. Morphologically identical, Poc and Pow are indistinguishable and commonly misidentified. Recent rises in the incidence of Poc/Pow infections have renewed efforts to address fundamental knowledge gaps in their biology, and to develop diagnostic tools to understand their epidemiological dynamics and malaria burden. A major roadblock has been the incompleteness of available reference assemblies (PocGH01, PowCR01; ~ 33.5 Mbp). Here, we applied multiple sequencing platforms and advanced bioinformatics tools to generate new reference genomes, Poc221 (South Sudan; 36.0 Mbp) and Pow222 (Nigeria; 34.3 Mbp), with improved nuclear genome contiguity (> 4.2 Mbp), annotation and completeness (> 99% Plasmodium spp., single copy orthologs). Subsequent sequencing of 6 Poc and 15 Pow isolates from Africa revealed a total of 22,517 and 43,855 high-quality core genome SNPs, respectively. Genome-wide levels of nucleotide diversity were determined to be 2.98 × 10^-4 (Poc) and 3.43 × 10^-4 (Pow), comparable to estimates for other Plasmodium species. Overall, the new reference genomes provide a robust foundation for dissecting the biology of Poc/Pow, their population structure and evolution, and will contribute to uncovering the recombination barrier separating these species.

Figure 1

Visualizing the new genomic references (A) Poc221 and (B) Pow222. From outer ring to inside: (1) Representation of each nuclear chromosome; (2) Black regions represent chromosomal specific islands of homology identified between the new and historic references. (3). Green regions represent core ortholog genes identified in the new references and Red regions represent members of the PIR multigene family. 4) SNP density.

Figure 2

Genomic Islands of homology identified between Poc221 (blue) and Pow222 (red) nuclear chromosomes. Regions located on equivalent chromosomes are shaded Orange, whilst translocated regions above 1kbp are shaded purple.

Figure 3

Neighbour joining tree of the 15 Pow and 6 Poc isolates from West Africa (red), Central Africa (green), East Africa (blue), when aligned to Pow222 and Poc221 respectively. Corresponding BioSample IDs can be found in Supplementary Table S6.