High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections
4 affiliations
- 1Tree of Life, Wellcome Sanger Institute, Hinxton, United Kingdom
- 2Swiss Tropical and Public Health Institute, Kreuzstrasse 2, Allschwil, Switzerland
- 3Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
- 4MIVEGEC, University of Montpellier, IRD, CNRS, Montpellier, France
Abstract
Malaria, caused by mosquito-transmitted Plasmodium parasites, remains a major global health challenge. While P. falciparum accounts for most malaria deaths, the lesser-studied P. ovale spp. and P. malariae also contribute to disease burden across many endemic regions, typically causing milder but chronic infections. Here, we generated high quality, chromosome-level reference genomes for P. ovale wallikeri, P. malariae, and P. falciparum directly from blood samples taken from natural infections. Using PacBio Ultra-Low-Input HiFi long-read sequencing and Hi-C chromatin conformation capture, we overcome limitations posed by low parasite biomass and the absence of in vitro culture for P. ovale wallikeri and P. malariae. These high quality reference genomes resolve previously inaccessible subtelomeric regions that include expanded gene families likely involved in host–parasite interactions, and they enhance our understanding of parasite persistence, transmission, immune evasion and comparative evolutionary studies. This work provides a critical foundation for including these neglected species in global malaria elimination efforts. Author summary: Our study presents high-quality, chromosome-level reference genomes for Plasmodium ovale, Plasmodium malariae and Plasmodium falciparum sampled directly from natural infections. While P. falciparum has been extensively studied due to its major role in severe malaria and global health burden, P. ovale spp. and P. malariae remain comparatively neglected with limited genomic resources, despite their wide distribution, chronic infections, and diagnostic challenges. Using PacBio Ultra Low Input HiFi long-read sequencing directly on enriched parasites from clinical samples collected in Mali, we overcome the challenges of low parasite biomass and the lack of in vitro culture systems for these neglected species. The resulting assemblies resolve previously inaccessible subtelomeric regions and reveal new insights into gene families implicated in host–parasite interactions. Alongside comprehensive gene annotations and structural insights, these resources lay the groundwork for better diagnostics, therapeutic target discovery, and comparative evolutionary studies of malaria parasites. This work provides tools to expand our understanding of P. ovale and P. malariae biology and provides an essential foundation for integrating these species into broader malaria research and elimination strategies.
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BibTeX
@article{dogga2026high,
title = {{High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections}},
author = {Sunil Kumar Dogga and Jesse C. Rop and Alex Makunin and Fiona Teltscher and Damon-Lee Pointon and Ying Sims and Marcela Uliano-Silva and James Torrance and Thomas C. Mathers and Jonathan M. D. Wood and Sekou Sissoko and Antoine Dara and Dinkorma T. Ouologuem and Arthur M. Talman and Abdoulaye A. Djimdé and Mara K. N. Lawniczak},
journal = {PLOS Pathogens},
year = {2026},
month = oct,
doi = {10.1371/journal.ppat.1014754},
url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014754},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections
AU - Sunil Kumar Dogga
AU - Jesse C. Rop
AU - Alex Makunin
AU - Fiona Teltscher
AU - Damon-Lee Pointon
AU - Ying Sims
AU - Marcela Uliano-Silva
AU - James Torrance
AU - Thomas C. Mathers
AU - Jonathan M. D. Wood
AU - Sekou Sissoko
AU - Antoine Dara
AU - Dinkorma T. Ouologuem
AU - Arthur M. Talman
AU - Abdoulaye A. Djimdé
AU - Mara K. N. Lawniczak
PY - 2026
DA - 2026/10/30
JO - PLOS Pathogens
DO - 10.1371/journal.ppat.1014754
UR - https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014754
AB - Malaria, caused by mosquito-transmitted Plasmodium parasites, remains a major global health challenge. While P. falciparum accounts for most malaria deaths, the lesser-studied P. ovale spp. and P. malariae also contribute to disease burden across many endemic regions, typically causing milder but chronic infections. Here, we generated high quality, chromosome-level reference genomes for P. ovale wallikeri, P. malariae, and P. falciparum directly from blood samples taken from natural infections. Using PacBio Ultra-Low-Input HiFi long-read sequencing and Hi-C chromatin conformation capture, we overcome limitations posed by low parasite biomass and the absence of in vitro culture for P. ovale wallikeri and P. malariae. These high quality reference genomes resolve previously inaccessible subtelomeric regions that include expanded gene families likely involved in host–parasite interactions, and they enhance our understanding of parasite persistence, transmission, immune evasion and comparative evolutionary studies. This work provides a critical foundation for including these neglected species in global malaria elimination efforts. Author summary: Our study presents high-quality, chromosome-level reference genomes for Plasmodium ovale, Plasmodium malariae and Plasmodium falciparum sampled directly from natural infections. While P. falciparum has been extensively studied due to its major role in severe malaria and global health burden, P. ovale spp. and P. malariae remain comparatively neglected with limited genomic resources, despite their wide distribution, chronic infections, and diagnostic challenges. Using PacBio Ultra Low Input HiFi long-read sequencing directly on enriched parasites from clinical samples collected in Mali, we overcome the challenges of low parasite biomass and the lack of in vitro culture systems for these neglected species. The resulting assemblies resolve previously inaccessible subtelomeric regions and reveal new insights into gene families implicated in host–parasite interactions. Alongside comprehensive gene annotations and structural insights, these resources lay the groundwork for better diagnostics, therapeutic target discovery, and comparative evolutionary studies of malaria parasites. This work provides tools to expand our understanding of P. ovale and P. malariae biology and provides an essential foundation for integrating these species into broader malaria research and elimination strategies.
SN - 1553-7374
ER -