Malaria in the 'Omics Era'

Abstract

Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth-the number of Plasmodium species' genomes sequenced-and in depth-massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.

Keywords: Plasmodium; genomics; malaria; methylation; methylomics.

Figure 1

Phylogeny of malaria parasites, showing the relationships among human-infecting species. The tree is a schematic diagram indicating topology (branch lengths are not to scale). The phylogenetic positions of human-infecting Plasmodium species are indicated. More detailed subtrees are shown for major lineages of simian malaria parasites and for the Laverania subgenus of ape parasites. Host species are indicated in brackets (hu = human; ma = macaque; ch = chimpanzee; go = gorilla). Tree topologies are after [4], and after [10] for the Laverania.

Figure 2

Plasmodium falciparum population genomics. (A) Map representing spread of the globally distributed species P. falciparum from sub-Saharan Africa to South America and Asia and the differing selection pressures that may drive local adaptation to different settings within and between continents: climatic and environmental conditions (sun and cloud); different vector species (the mosquito); differing treatment regimes (the pill). Below the map is a schematic population structure tree based on genome-wide variation data, after [48]. (Regional populations are indicated at the tips of the tree: SAm = South America; WA = West Africa; CA = Central Africa; EA = East Africa; SAs = South Asia; SEA,W = South East Asia, West; SEA,W = South East Asia, East; O = Oceania). (B) Representation of a genome-wide scan for signatures of selection. Indices (e.g., homozygosity or linkage disequilibrium within a population, F_ST among populations, etc.) are plotted on the y-axis across all chromosomes on the x-axis (here, for P. falciparum’s 14 chromosomes) to identify outlier regions, such as the chloroquine resistance transporter gene (crt) region on chromosome 7 shown here. Data points could be individual variant sites, genes or other chromosomal regions, depending upon the index being plotted. By highlighting outliers compared to a genomic average, confounding effects of population histories can be avoided.

Figure 3

Epigenomics in Plasmodium. (A) Cytosine can be converted to 5-Methylcytosine (5mC) by DNA methyltransferase (DNMT), and 5mC to 5-Hydroxymethylcytosine (5hmC) by Ten-eleven translocation methylcytosine dioxygenase (TET), which also converts 5hmC to 5-formylcytosine (5fC) and 5fC to 5-carboxylcytosine (5caC). Uracil-DNA glycosylase (TDG) and base-excision repair (BER) converts 5caC back to (unmethylated) cytosine. (B) The standard genomic method to detect 5mC (bisulfite treatment to convert unmethylated C to uracil, seen as a T in the final sequencing library, followed by whole genome sequencing) cannot distinguish 5mC from 5hmC. The addition of an oxidation step, converting 5hmC to 5fC (which bisulfite treatment does convert to uracil) can allow 5hmC to be detected and quantified. This approach suggests the majority of methylated C in Plasmodium is 5hmC. (C) Epigenetic marks (black lines with red circles) are shown on a stretch of DNA (grey = intergenic/intronic; black = exonic). In Plasmodium, exonic sequence near to intron-exon boundaries is enriched for these modified cytosines. Possible functional consequences include gene silencing or upregulation, and alternative splicing. Genome-wide patterns of methylation could act as alternative markers for gene expression.