De novo genome assembly of Plasmodium knowlesi from contemporary clinical isolates - a novel scalable resource to take forward malaria research

Abstract

Plasmodium knowlesi is a zoonotic malaria parasite of Southeastern macaque monkeys that causes zoonotic malaria in humans. P. knowlesi is also an experimental model for malaria, and information on P. knowlesi largely stem from experimental lines first isolated >four decades ago, rather than contemporary isolates causing human infections. The experimental lines are laboratory-restricted and have become relatively genetically stagnant and free from the selection pressure that would naturally occur in nature. Within the P. knowlesi genome exist the Schizont Infected Cell Agglutination variant antigen (SICAvar) and Plasmodium knowlesi interspersed repeat (kir) multigene families significant, which are of biological and scientific interest. To provide context using contemporary clinical isolates, this project aimed to generate high-quality genome sequences using long-sequencing from clinical ‘wild-type’ samples from infected patients. This includes generating new information on variant multigene families in P. knowlesi genomes generated from clinical patient whole blood. The work presented here details a method to deplete leucocytes in thawed P. knowlesi-infected patient whole blood samples to generate parasite-enriched DNA for whole-genome sequencing, resulting in >95% human DNA reduction. The extracted DNA was sequenced with long-read sequencing technology to create de novo whole-genome assemblies. From these, two isolate genomes representing the two dimorphic clusters of P. knowlesi in clinical samples were analysed. The generated genomes are highly syntenic to the published reference genome, sharing >4500 orthologous clusters with the PKNH reference genome. However, the number of SICAvar and kir genes present in the dataset deviated from the published reference genomes of P. knowlesi. The successful generation and construction of these patient genomes aid further interrogation of the contemporary P. knowlesi genome, with a focus on the constituent genes present in comparison to the experimental line.