Population Genomic Scan for Candidate Signatures of Balancing Selection to Guide Antigen Characterization in Malaria Parasites

Abstract

Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome) had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs) for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3), and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%), indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing selection are now prioritized for functional study.

The Merozoite Surface Protein 1 Complex Is a Platform for Binding to Human Erythrocytes by Plasmodium falciparum

“…The DBL domains of MSPDBL1 and MSPDBL2 are extremely polymorphic, indicating that they are under high levels of selective pressure presumably from the host immune system (27)(28)(29). This is indicative of the important roles of the DBL domains within MSPDBL1 and -2 and is consistent with the inability to disrupt the function of both within the same parasite.…”

“…This function suggests that they may be involved in the initial interaction of the merozoite with the host erythrocyte, and the ability of antibodies to MSPDBL1 to partially inhibit parasite growth is consistent with this (25). These proteins appear to be functionally important to parasite survival as they have been shown to be under balancing selection with one of the strongest selection signatures for P. falciparum proteins observed for MSPDBL2 (27,28). Importantly, naturally acquired antibodies against the highly polymorphic DBL domain of MSPDBL2 have been shown to be significantly associated with protection from malaria (29).…”

Malaria Genomics in the Era of Eradication

“…Such work illuminated the recent demographic history of multiple parasite and vector species, defined sometimes complex gene flow boundaries, and revealed the impact of immune, drug, or insecticide selection on the genomes of malaria parasites and vectors. Subsequently, more comprehensive characterizations of genetic diversity have yielded thorough inventories of genomic diversity across many geographic regions (Amambua-Ngwa et al 2012;Manske et al 2012;Miotto et al 2013Miotto et al , 2015 MalariaGEN P. falciparum Community Project 2016), refining our understanding of population boundaries and diversity differences between populations. Collectively, this deep genomic sequencing dataset, for example, represented in the open-access Pf3k collaboration and database (www.malariagen.net/projects/ pf3k), facilitates informed development of markers for genotyping to analyze even larger sample collections.…”

Malaria life cycle intensifies both natural selection and random genetic drift

“…M alaria, which is caused by the parasite Plasmodium falciparum, is one of the major causes of death worldwide. To aid the development of vaccines and drug treatments for malaria, researchers have studied the P. falciparum genome and identified genes that are essential to malaria parasites as well as genes that are related to drug-resistance phenotypes using population genetic tools (1)(2)(3)(4)(5)(6). Researchers have also focused on particular genes related to drug resistance and characterized the evolutionary pathways of emerging drug resistance using Escherichia coli and Saccharomyces cerevisiae as model systems (7)(8)(9)(10).…”