De novo assembly of Plasmodium knowlesi genomes from clinical samples explain the counterintuitive intrachromosomal organization of variant SICAvar and kir multiple gene family members
Abstract
Plasmodium knowlesi, a malaria parasite of Old World macaque monkeys, is used extensively to model Plasmodium biology. Recently, P. knowlesi was found in the human population of Southeast Asia, particularly Malaysia. P. knowlesi causes uncomplicated to severe and fatal malaria in the human host with features in common with the more prevalent and virulent malaria caused by Plasmodium falciparum. As such, P. knowlesi presents a unique opportunity to develop experimental translational model systems for malaria pathophysiology informed by clinical data from same-species human infections. Experimental lines of P. knowlesi represent well-characterized genetically stable parasites, and to maximize their utility as a backdrop for understanding malaria pathophysiology, genetically diverse contemporary clinical isolates, essentially wild-type, require comparable characterization. The Oxford Nanopore PCR-free long-read sequencing platform was used to sequence and de novo assemble P. knowlesi genomes from frozen clinical samples. The sequencing platform and assembly pipelines were designed to facilitate capturing data and describing, for the first time, P. knowlesi schizont-infected cell agglutination (SICA) var and Knowlesi-Interspersed Repeats (kir) multiple gene families in parasites acquired from nature. The SICAvar gene family members code for antigenically variant proteins analogous to the virulence-associated P. falciparum erythrocyte membrane protein (PfEMP1) multiple var gene family. Evidence presented here suggests that the SICAvar family members have arisen through a process of gene duplication, selection pressure, and variation. Highly evolving genes including PfEMP1family members tend to be restricted to relatively unstable sub-telomeric regions that drive change with core genes protected in genetically stable intrachromosomal locations. The comparable SICAvar and kir gene family members are counter-intuitively located across chromosomes. Here, we demonstrate that, in contrast to conserved core genes, SICAvar and kir genes occupy otherwise gene-sparse chromosomal locations that accommodate rapid evolution and change. The novel methods presented here offer the malaria research community not only new tools to generate comprehensive genome sequence data from small clinical samples but also new insight into the complexity of clinically important real-world parasites.
Citation
Oresegun , D R , Thorpe , P , Benavente , E D , Campino , S , Fauzi , M , Moon , R W , Clark , T G & Cox-Singh , J 2022 , ' De novo assembly of Plasmodium knowlesi genomes from clinical samples explain the counterintuitive intrachromosomal organization of variant SICAvar and kir multiple gene family members ' , Frontiers in Genetics , vol. 13 , 855052 . https://doi.org/10.3389/fgene.2022.855052
Publication
Frontiers in Genetics
Status
Peer reviewed
ISSN
1664-8021Type
Journal article
Rights
Copyright © 2022 Oresegun, Thorpe, Benavente, Campino, Muh, Moon, Clark and Cox-Singh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Description
DRO is supported by the Wellcome Trust ISSF award https://wellcome.org/what-we- do/our-work/institutional-strategic-support-fund 204821/Z/16/Z. Bioinformatics and computational biology analyses were supported by the University of St Andrews Bioinformatics Unit (AMD3BIOINF), funded by Wellcome Trust ISSF https://wellcome.org/what-we-do/our-work/institutional-strategic-support-fund award 105621/Z/14/Z and 204821/Z/16/Z. JCS - The sample BioBank was compiled with informed consent (Medial Research Council, www.mrc.ac.uk, grant G0801971). JCS - Genome sequencing was supported by Tenovus Scotland (https://tenovus- scotland.org.uk T16/03). TGC is funded by the Medical Research Council UK www.mrc.ac.uk (Grant no. MR/M01360X/1, MR/N010469/1, MR/R025576/1, and MR/R020973/1) and BBSRC (Grant no. BB/R013063/1). SC is funded by Medical Research Council UK grants www.mrc.ac.uk (ref. MR/M01360X/1, MR/R025576/1, and MR/R020973/1).Collections
Items in the St Andrews Research Repository are protected by copyright, with all rights reserved, unless otherwise indicated.