Constructing a Pangenome Reference for Nigerian Plasmodium falciparum Populations: Structural Variation, Antigen Diversity, and Vaccine Escape Architecture

Pangenome references, which capture the full complement of core and accessory genomic content across a population of genomes, are transforming our understanding of pathogen genetic diversity and have direct implications for vaccine target selection. For Plasmodium falciparum, the causative agent of the most lethal form of malaria, a Nigeria-specific pangenome is absent, leaving critical gaps in understanding local antigen diversity and vaccine escape potential. This dissertation constructs the first pangenome reference for Nigerian P. falciparum using isolates spanning five geopolitical zones. A total of 120 P. falciparum clinical isolates from Kano, Lagos, Enugu, Rivers, Benue, and Borno States were cultured to sufficient parasitemia. High-molecular-weight DNA was extracted and sequenced using Pacific Biosciences HiFi long-read technology to enable gapless genome assembly. Pangenome graphs were constructed using Minigraph-Cactus and annotated with a custom variant-aware pipeline. Antigen gene family analysis focused on var, rifin, stevor, and pfmc-2tm families using PanOCT clustering. The resulting pangenome comprised a core genome (present in greater than 95% of isolates) of 4,821 genes and an accessory genome of 1,134 gene clusters. Structural variant analysis identified 312 inversions and 87 novel translocations not present in the 3D7 reference. PfEMP1 var gene diversity analysis revealed 14 domain cassette architectures unique to Nigerian isolates with no representation in existing vaccine antigen databases. These domain variants were computationally assessed as likely immune evasion-competent structures. This pangenome resource represents a foundational contribution to Nigerian malaria genomics and vaccine development. Keywords: pangenome, Plasmodium falciparum, PfEMP1, structural variation, Nigeria.