Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade

Abstract

P. cynomolgi, a malaria-causing parasite of Asian Old World monkeys, is the sister taxon of P. vivax, the most prevalent malaria-causing species in humans outside of Africa. Because P. cynomolgi shares many phenotypic, biological and genetic characteristics with P. vivax, we generated draft genome sequences for three P. cynomolgi strains and performed genomic analysis comparing them with the P. vivax genome, as well as with the genome of a third previously sequenced simian parasite, Plasmodium knowlesi. Here, we show that genomes of the monkey malaria clade can be characterized by copy-number variants (CNVs) in multigene families involved in evasion of the human immune system and invasion of host erythrocytes. We identify genome-wide SNPs, microsatellites and CNVs in the P. cynomolgi genome, providing a map of genetic variation that can be used to map parasite traits and study parasite populations. The sequencing of the P. cynomolgi genome is a critical step in developing a model system for P. vivax research and in counteracting the neglect of P. vivax.

Figure 1. Architecture of the P. cynomolgi genome and associated genome-wide variation data.

Data are shown for each of the 14 P. cynomolgi chromosomes. The six concentric rings, from outermost to innermost, represent (i) the location of 5,049 P. cynomolgi genes, excluding those on small contigs (cyan lines); (ii) genome features, including 14 centromeres (thick black lines), 43 telomeric sequence repeats (short red lines), 43 tRNA genes (red lines), 10 rRNAs (dark blue lines) and several gene family members, including 53 cyir (dark green lines), 8 rbp (brown lines), 13 sera (serine-rich antigen; pink lines), 25 trag (tryptophan-rich antigen; purple lines), 12 msp3 (merozoite surface protein 3; light gray lines), 13 msp7 (merozoite surface protein 7; gray lines), 25 rad (silver lines), 8 etramp (orange lines), 16 Pf-fam-b (light blue lines) and 7 Pv-fam-d (light green lines); (iii) plot of d_S/d_N for 4,605 orthologs depicting genome-wide polymorphism within P. cynomolgi strains B and Berok (black line) and divergence between P. cynomolgi strains B and Berok and P. vivax Salvador I (red line); a track above the plot indicates P. cynomolgi genes under positive selection (red) and purifying selection (blue), and a track below the plot indicates P. cynomolgi–P. vivax orthologs under positive selection (red) and purifying selection (blue); (iv) heatmap indicating SNP density of 3 P. cynomolgi strains plotted per 10-kb windows: red, 0–83 SNPs per 10 kb (regions of lowest SNP density); blue, 84–166 SNPs per 10 kb; green, 167–250 SNPs per 10 kb; purple, 251–333 SNPs per 10 kb; orange, 334–416 SNPs per10 kb; yellow, 417–500 SNPs per10 kb (regions of highest SNP density); (v) log₂ ratio plot of CNVs identified from a comparison of P. cynomolgi strains B and Berok; and (vi) map of 182 polymorphic intergenic microsatellites (MS, black dots). The figure was generated using Circos software (see URLs).

Figure 2. Genome synteny between six species of Plasmodium parasite.

Protein-coding genes of P. cynomolgi are shown aligned with those of five other Plasmodium genomes: two species belonging to the monkey malaria clade, P. vivax and P. knowlesi; two species of rodent malaria, P. berghei and P. chabaudi; and P. falciparum. Highly conserved protein-coding regions between the genomes are colored in order from red (5′ end of chromosome 1) to blue (3′ end of chromosome 14) with respect to genomic position of P. cynomolgi.

Figure 3. Comparison of the genes of P. cynomolgi, P. vivax and P. knowlesi.

The Venn ellipses represent the three genomes, with the total number of genes assigned to the chromosomes indicated under the species name. Cylinders depict orthologous and non-orthologous genes between the three genomes, with the number of genes in each indicated and represented graphically by cylinder relative width. In each cylinder, genes are divided into three categories whose thickness is represented by colored bands proportional to category percentage.