Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
UK Health Security Agency, Malaria Reference Laboratory, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
Sci Rep. 2024 Feb 15;14(1):3843. doi: 10.1038/s41598-024-54382-5.
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 (Poc) and 3.43 × 10 (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.
尽管卵形疟原虫（Poc）和沃利氏疟原虫（Pow）是广泛分布于非洲和亚洲的重要人类感染疟原虫，但对它们的基因组多样性知之甚少。形态上相同，Poc 和 Pow 无法区分，通常被错误识别。最近 Poc/Pow 感染病例的增加，促使人们重新努力解决其生物学方面的基本知识差距，并开发诊断工具，以了解其流行病学动态和疟疾负担。一个主要的障碍是现有的参考组装（PocGH01，PowCR01；~33.5 Mbp）不完整。在这里，我们应用多种测序平台和先进的生物信息学工具来生成新的参考基因组，Poc221（南苏丹；36.0 Mbp）和 Pow222（尼日利亚；34.3 Mbp），核基因组连续性（>4.2 Mbp）、注释和完整性（>99%的疟原虫属，单拷贝直系同源物）得到了改善。随后对来自非洲的 6 株 Poc 和 15 株 Pow 分离株进行测序，分别发现了总共 22517 个和 43855 个高质量的核心基因组 SNP。全基因组核苷酸多样性水平分别确定为 2.98×10（Poc）和 3.43×10（Pow），与其他疟原虫属的估计值相当。总的来说，新的参考基因组为剖析 Poc/Pow 的生物学特性、它们的种群结构和进化提供了一个强大的基础，并将有助于揭示将这两个物种分开的重组障碍。
