A Plasmodium falciparum Pangenome Resource to Drive Structural Variant Discovery and to assist Malaria Control

Plasmodium falciparum, the deadliest causative agent of malaria, harbours extensive structural variation that underlies key biological processes including drug resistance and diagnostic evasion. Here, we present PfPan, a P. falciparum pangenome constructed from 13 geographically diverse high-quality reference genomes using Minigraph-Cactus, adding 4.7 Mb of sequence beyond the 3D7 linear reference. We identify over 5,000 structural variants across the reference genomes and demonstrate improved genotyping using the vg toolkit compared to linear reference-based approaches, with comparable performance for small variant discovery. Benchmarking against assembly-derived truth sets confirms pangenome superiority for structural variant detection, particularly at complex and hypervariable loci. Applying PfPan to 878 globally sampled P. falciparum whole-genome sequences, we characterise the population-level frequency of clinically relevant structural variants, including a high-frequency 10.4 kb insertion at the drug resistance-linked gch1 locus, and explore deletions upstream of the gene encoding the diagnostic target HRP2. PfPan provides a foundational resource for reducing reference bias in P. falciparum genomic surveillance and offers a framework for improved detection of variants relevant to drug resistance and malaria control.