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Peer-reviewedCC BY 4.0G3: Genes, Genomes, Genetics

De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology

  • Prince B Nyarko1
  • Mathieu Quenu1
  • Marc-Antoine Guéry1
  • Camille Cohen1
  • Godfrey Kinyori Wagutu1
  • William L Hamilton2,3,4
  • Sophia T Girgis4
  • Alex Makunin5
  • Shane A McCarthy5
  • Mara K N Lawniczak5
  • Antoine Claessens1,6
6 affiliations
  1. 1LPHI, CNRS, INSERM, University of Montpellier , Montpellier 34090 ,
  2. 2University of Cambridge, Department of Medicine , Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ ,
  3. 3Cambridge University Hospitals NHS Foundation Trust , Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ ,
  4. 4Wellcome Sanger Institute , Wellcome Trust Genome Campus, Hinxton, CB10 1RQ ,
  5. 5Tree of Life, Wellcome Sanger Institute , Hinxton CB10 1SA ,
  6. 6Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine , Banjul, The Gambia
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Abstract

Plasmodium falciparum possesses a highly structured genome with extensive sequence diversity concentrated in Variant Surface Antigen (VSA) families. These genes—var, rif, and stevor—play key roles in immune evasion and pathogenesis and are difficult to assemble using short-read sequencing technologies. Here, we applied PacBio HiFi long-read sequencing to generate high-quality de novo genome assemblies from 43 P. falciparum parasite cultures originating from community cases in The Gambia. Parasites were culture-adapted, cloned by limiting dilution where possible, and sequenced using high molecular weight DNA extracts. Assemblies from single-genotype lineages were constructed using hifiasm, producing complete chromosomal-length scaffolds with high base accuracy without requiring short-read polishing. We recovered full repertoires of var, rif, and stevor genes and classified them into known subgroups. Together, our results demonstrate that PacBio HiFi sequencing enables accurate assembly of complex P. falciparum genomes from natural infections. This work provides a valuable genomic resource for future studies of parasite evolution, transmission dynamics, and antigenic diversity, and suggests that VSA repertoires can serve as reliable proxies of genetic relatedness across infections.

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Cite

BibTeXRIS
BibTeX
@article{nyarko2026novo,
  title = {{De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology}},
  author = {Prince B Nyarko and Mathieu Quenu and Marc-Antoine Guéry and Camille Cohen and Godfrey Kinyori Wagutu and William L Hamilton and Sophia T Girgis and Alex Makunin and Shane A McCarthy and Mara K N Lawniczak and Antoine Claessens},
  journal = {G3: Genes, Genomes, Genetics},
  year = {2026},
  month = oct,
  doi = {10.1093/g3journal/jkag302},
  url = {https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag302/9002698},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology
AU  - Prince B Nyarko
AU  - Mathieu Quenu
AU  - Marc-Antoine Guéry
AU  - Camille Cohen
AU  - Godfrey Kinyori Wagutu
AU  - William L Hamilton
AU  - Sophia T Girgis
AU  - Alex Makunin
AU  - Shane A McCarthy
AU  - Mara K N Lawniczak
AU  - Antoine Claessens
PY  - 2026
DA  - 2026/10/27
JO  - G3: Genes, Genomes, Genetics
DO  - 10.1093/g3journal/jkag302
UR  - https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag302/9002698
AB  - Plasmodium falciparum possesses a highly structured genome with extensive sequence diversity concentrated in Variant Surface Antigen (VSA) families. These genes—var, rif, and stevor—play key roles in immune evasion and pathogenesis and are difficult to assemble using short-read sequencing technologies. Here, we applied PacBio HiFi long-read sequencing to generate high-quality de novo genome assemblies from 43 P. falciparum parasite cultures originating from community cases in The Gambia. Parasites were culture-adapted, cloned by limiting dilution where possible, and sequenced using high molecular weight DNA extracts. Assemblies from single-genotype lineages were constructed using hifiasm, producing complete chromosomal-length scaffolds with high base accuracy without requiring short-read polishing. We recovered full repertoires of var, rif, and stevor genes and classified them into known subgroups. Together, our results demonstrate that PacBio HiFi sequencing enables accurate assembly of complex P. falciparum genomes from natural infections. This work provides a valuable genomic resource for future studies of parasite evolution, transmission dynamics, and antigenic diversity, and suggests that VSA repertoires can serve as reliable proxies of genetic relatedness across infections.
SN  - 2160-1836
ER  -