Evolutionary analysis of the most polymorphic gene family in falciparum malaria.

Thomas D Otto,Mandy J Sanders,Matt Berriman,Dominic Kwiatkowski,Sammy A Assefa,Ulrike Böhme,Chris Newbold

doi:10.12688/wellcomeopenres.15590.1

Abstract

The var gene family of the human malaria parasite Plasmodium falciparum encode proteins that are crucial determinants of both pathogenesis and immune evasion and are highly polymorphic. Here we have assembled nearly complete var gene repertoires from 2398 field isolates and analysed a normalised set of 714 from across 12 countries. This therefore represents the first large scale attempt to catalogue the worldwide distribution of var gene sequences We confirm the extreme polymorphism of this gene family but also demonstrate an unexpected level of sequence sharing both within and between continents. We show that this is likely due to both the remnants of selective sweeps as well as a worrying degree of recent gene flow across continents with implications for the spread of drug resistance. We also address the evolution of the var repertoire with respect to the ancestral genes within the Laverania and show that diversity generated by recombination is concentrated in a number of hotspots. An analysis of the subdomain structure indicates that some existing definitions may need to be revised From the analysis of this data, we can now understand the way in which the family has evolved and how the diversity is continuously being generated. Finally, we demonstrate that because the genes are distributed across the genome, sequence sharing between genotypes acts as a useful population genetic marker.

Highlights

Plasmodium falciparum is the most virulent of the human malaria parasites, at least in part because it can concentrate in the small vasculature of organs via its ability to adhere to endothelial cells leading to organ dysfunction
The var genes encode a family of proteins called Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) that are expressed on the surface of infected red cells in a mutually exclusive fashion[1]
Using whole genome sequencing data from approximately 2,400 clinical isolates of Plasmodium falciparum produced by the Pf3K project (Extended data: Table S1), we developed a pipeline (Methods) that enabled us to assemble contigs representing putative individual var exons

Summary

Introduction

Plasmodium falciparum is the most virulent of the human malaria parasites, at least in part because it can concentrate in the small vasculature of organs via its ability to adhere to endothelial cells leading to organ dysfunction. On the red cell surface, PfEMP1 proteins mediate both adherence to endothelium and induce host protective antibodies The latter are evaded through transcriptional switches among the var gene family such that new sequences are periodically expressed. A more extensive analysis of full-length genes from the sequenced genomes of seven laboratory-adapted isolates revealed that all domain subclasses can be further divided into a number of subdomain types and that in some cases these can be grouped together into “domain cassettes”[13] Some of these domain cassettes (DC) are associated with binding to specific receptors on endothelial cells; for instance, var genes containing DC8 and 13 are expressed in parasites causing severe malaria and bind to endothelial protein C receptor (EPCR)[14]. RNAseq of parasites isolated from severe and non-severe patients in Indonesia has been used to assemble expressed var gene sequences[17]

Methods

Results

Discussion

Conclusion