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Plasmodium cynomolgi, a malaria parasite of Asian Old World monkeys, is the sister taxon of Plasmodium vivax, the most prevalent human malaria species outside Africa. Since P. cynomolgi shares many phenotypic, biologic and genetic characteristics of P. vivax, we generated draft genome sequences of three P. cynomolgi strains and performed comparative genomic analysis between them and P. vivax, as well as a third previously sequenced simian parasite, Plasmodium knowlesi. Here we show that genomes of the monkey malaria clade can be characterized by 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 for mapping parasite traits and studying parasite populations. The P. cynomolgi genome is a critical step in developing a model system for P. vivax research, and to counteract the neglect of P. vivax.
Human malaria is transmitted by anopheline mosquitoes and caused by four species in the genus Plasmodium. Of these, Plasmodium vivax is the major malaria agent outside Africa, annually causing 80 to 100 million cases1. Often mistakenly regarded as benign and self-limiting, P. vivax treatment and control present challenges distinct from those of the more virulent P. falciparum. Biological traits including a dormant (hypnozoite) liver stage responsible for recurrent infections (relapses), early infective sexual stages (gametocytes), and transmission from low parasite densities in the blood2, coupled with emerging antimalarial drug resistance3, render P. vivax resilient to modern control strategies. Recent evidence indicates that P. falciparum derives from parasites of great apes in Africa4, while P. vivax is more closely related to parasites of Asian Old World monkeys (OWM)5–7, though not itself infective to OWM.
P. vivax cannot be cultured in vitro, and the small New World monkeys capable of hosting it are rare and do not provide an ideal model system. P. knowlesi, an Asian OWM parasite recently recognized as a significant zoonosis for humans8, offers a sequenced genome9, but the species is distantly related to P. vivax and phenotypically dissimilar. In contrast, P. cynomolgi, a simian parasite which can infect humans experimentally10, is the closest living relative (i.e., a sister taxon) to P. vivax and possesses most of its genetic, phenotypic, and biologic characteristics: importantly, periodic relapses caused by dormant hypnozoites, early infectious gametocyte formation, and invasion of Duffy blood group-positive reticulocytes. P. cynomolgi thus offers a robust model for P. vivax in a readily-available laboratory host, the Rhesus monkey, whose genome was recently sequenced11. Here we report draft genome sequences of three P. cynomolgi strains, and comparative genomic analyses of P. cynomolgi, P. vivax12 and P. knowlesi9, three members of the monkey malaria clade.
We sequenced the genome of P. cynomolgi ‘B’ strain, isolated from a monkey in Malaysia and grown in splenectomized monkeys (Online Methods). A combination of Sanger, Roche 454 and Illumina chemistries was deployed to generate a high quality reference assembly at 161-fold coverage, consisting of 14 supercontigs (corresponding to the 14 parasite chromosomes) and ~1,649 unassigned contigs, comprising a total length of ~26.2 Mb (Supplementary Table 1). Comparing genomic features of P. cynomolgi, P. knowlesi and P. vivax reveals many similarities, including GC content (mean GC 40.5%), fourteen conserved centromeres, and presence of intrachromosomal telomeric sequences (ITSs; GGGTT[T/C]A) discovered in the P. knowlesi genome9 but absent in P. vivax (Table 1, Supplementary Table 2 and Fig. 1).
We annotated the P. cynomolgi strain B genome using a combination of ab initio gene prediction programs trained on high quality datasets and sequence similarity searches against the annotated P. vivax and P. knowlesi genomes. Unsurprisingly for species from the same monkey malaria clade, gene synteny along the 14 chromosomes is highly conserved, though numerous microsyntenic breaks occur in regions containing multigene families (Fig. 2 and Table 2). The P. cynomolgi genome contains 5,722 genes, of which about half encode conserved hypothetical proteins of unknown function, as is the case in all Plasmodium genomes sequenced to date. A maximum likelihood (ML) phylogenetic tree using 192 conserved ribosomal and translation/transcription-related genes (Supplementary Figure 1) confirms the close relationship of P. cynomolgi to P. vivax compared to five other Plasmodium species. Approximately 90% of genes (4,613) have reciprocal best match orthologs in all three species (Fig. 3), enabling refinement of the existing P. vivax and P. knowlesi annotations (Supplementary Table 3). The high degree of gene orthology enabled us to identify specific examples of gene duplication (an important vehicle for genome evolution), including a P. cynomolgi duplicated homolog of P. vivax Pvs28, a sexual stage surface antigen that is a transmission-blocking vaccine candidate13 (Supplementary Table 4). Genes common only to P. cynomolgi and P. vivax (n = 214) outnumber those exclusive to P. cynomolgi and P. knowlesi (n = 100) or P. vivax and P. knowlesi (n = 17). Such figures establish the utility of P. cynomolgi as a model species for studying the more intractable P. vivax.
Remarkably, most of the genes specific to a particular species belong to multigene families (excluding hypothetical genes; Table 2 and Supplementary Table 5). This suggests repeated lineage-specific gene duplication and/or gene deletion in multigene families within the three monkey malaria clade species. Moreover, copy number of multigene families was generally greater in the P. cynomolgi/P. vivax lineage than in P. knowlesi, suggesting repeated gene duplication in the ancestral lineage of P. cynomolgi/P. vivax (or repeated gene deletion in the P. knowlesi lineage). Thus the genomes of P. cynomolgi, P. vivax and P. knowlesi can almost be completely characterized by variations in the copy number of multigene families. Examples of such families include those that encode proteins involved in evasion of the human immune system (vir, kir and SICAvar), and invasion of host red blood cells (dbp and rbp), described below.
In malaria parasites, invasion of host erythrocytes, mediated by specific interactions between parasite ligands and erythrocyte receptors, is a crucial component of the parasite life-cycle. Of great interest are the ebl and rbl families, which encode parasite ligands required for the recognition of host erythrocytes. The ebl genes encode erythrocyte binding-like (EBL) ligands such as the Duffy binding proteins (DBP) that bind to Duffy Antigen/Receptor for Chemokines (DARC) on human and monkey erythrocytes. The rbl genes encode the reticulocyte binding-like (RBL) protein family, including reticulocyte binding proteins (RBPs) in P. cynomolgi and P. vivax, and normocyte binding proteins (NBPs) in P. knowlesi, which bind to unknown erythrocyte receptors14. We confirmed the presence of two dbp genes in P. cynomolgi15 (Supplementary Table 6), in contrast to the one dbp and three dbp genes identified in P. vivax and P. knowlesi, respectively. This raises an intriguing hypothesis -- that P. vivax lost one dbp gene, and hence its infectivity to OWM erythrocytes, after divergence from a common P. vivax/P. cynomolgi ancestor. This hypothesis is also supported by our identification of only single copies of dbp genes in two other closely related OWM malaria parasites P. fieldi and P. simiovale, which are incapable of infecting humans16. These latter OWM species lost one or more dbp genes during divergence that conferred infectivity to humans, while P. cynomolgi and P. knowlesi retained dbp genes that allow invasion of human erythrocytes (Supplementary Figure 2).
We found multiple rbp genes, some truncated or present as pseudogenes, in the P. cynomolgi genome (Fig. 1 and Table 2). Phylogenetic analysis shows that rbls from P. cynomolgi, P. vivax and P. knowlesi can be classified into three distinct groups, RBP/NBP-1, RBP/NBP-2 and RBP/NBP-3 (Supplementary Figure 3), and suggests that these groups existed before the three species diverged. All three groups of RBP/NBP are represented in P. cynomolgi, whereas P. vivax and P. knowlesi lack functional genes of the RBP/NBP-3 and RBP/NBP-1 groups, respectively. Thus rbl gene family expansion appears to have occurred after speciation, indicating that the three species have multiple species-specific erythrocyte invasion mechanisms. Intriguingly, we found an ortholog of P. vivax rbp1b in some strains of P. cynomolgi, but not in others (Supplementary Table 6). This is the first example of an rbp copy number variant between strains of a single Plasmodium species that we are aware of, and highlights how repeated birth and death of rbl genes, a signature of adaptive evolution, may have enabled species of the monkey malaria clade to expand or switch hosts between monkeys and humans.
The largest gene family in P. cynomolgi, consisting of 256 cyir (cynomolgi interspersed repeat) genes, is part of the pir (plasmodium interspersed repeat) superfamily that include P. vivax virs (n = 319) and P. knowlesi kirs (n = 70; Table 2). Pir proteins reside on the surface of infected erythrocytes and play an important role in immune evasion17. Most cyir genes have sequence similarity to P. vivax vir genes (n = 254; Supplementary Table 7) and are found in subtelomeric regions (Fig. 1), but interestingly 11 cyirs have sequence similarity to P. knowlesi kirs (Supplementary Table 7) and occur internally as the kirs do in P. knowlesi. As with the ‘molecular mimicry’ in P. knowlesi9, one CYIR protein (PCYB_032250) has a 56-amino acid region highly similar to the extracellular domain of primate CD99 (Supplementary Figure 4), a molecule involved in the regulation of T-cell function. A novel finding is that P. cynomolgi has two genes whose sequences are similar to P. knowlesi SICAvar genes (Supplementary Table 7) that are expressed on the surfaces of schizont-infected macaque erythrocytes and are involved in antigenic variation18.
The ability to form a dormant hypnozoite stage is common to both P. cynomolgi and P. vivax, and was first shown in laboratory infections of monkeys by mosquito-transmitted P. cynomolgi19. In a search for candidate hypnozoite genes, we identified nine coding for ‘dormancy-related’ proteins and possessing ApiAP2 motifs20 necessary for stage-specific transcriptional regulation at the sporozoite (pre-hypnozoite) stage (Supplementary Table 8). The candidates include kinases that are involved in cell-cycle transition; hypnozoite formation may be regulated by phosphorylation of proteins specifically expressed at the pre-hypnozoite stage. Our list of P. cynomolgi candidate genes represents an informed starting point for experimental studies on this elusive stage.
We sequenced P. cynomolgi strains Berok (from Malaysia) and Cambodian (from Cambodia) to 26× and 17 coverage, respectively, to characterize P. cynomolgi genome-wide diversity through analysis of SNPs, CNVs and microsatellites. A comparison of the three P. cynomolgi strains identified 178,732 SNPs (Supplementary Table 9), a frequency of one SNP per 151 bp, a polymorphism level somewhat similar to that found when P. falciparum genomes are compared21,22. We calculated the pairwise nucleotide diversity (π) as 5.41 × 10−3 across the genome, which varies little between the chromosomes. We assessed genome-wide copy number variants (CNVs) between P. cynomolgi B and Berok strains, using a robust statistical model in the program CNV-seq23, identifying 1,570 CNVs (1 per 17 kb), including one containing the rbp1b gene on chromosome 7 described above (Supplementary Figure 5). Finally, mining of P. cynomolgi B and Berok strains identified 182 polymorphic intergenic microsatellites (Supplementary Table 10), the first set of genetic markers developed for this species. These provide a toolkit for genetic diversity and population structure studies of laboratory stocks or natural infections of P. cynomolgi, many of which have recently been isolated from screening hundreds of wild monkeys for the zoonosis P. knowlesi24.
We estimated the difference between the number of synonymous changes per synonymous site (Ds) and the number of non-synonymous changes per non-synonymous site (Dn) over 4,605 pairs of orthologs within P. cynomolgi strain B and Berok, and between these two P. cynomolgi genomes and P. vivax Salvador I, using a simple Nei-Gojobori model25. We found 196 genes with Dn > Ds within the two P. cynomolgi strains, and 1,742 genes with Ds > Dn (Supplementary Table 11). Genes with relatively high Dn > Ds include transmembrane proteins such as antigens and transporters, among which is a transmission blocking target antigen Pcyn230 (PCYB_042090). Interestingly, the P. vivax ortholog (PVX_003905) does not show evidence for positive selection26, suggesting species-specific positive selection. We explored the degree to which evolution of orthologs has been constrained between P. cynomolgi and P. vivax, and found 154 genes under possible accelerated evolution but 1,613 genes under possible purifying selection (Supplementary Table 12). This conservative estimate indicates that at least 35% of loci have diverged under strong constraint, compared with 3.3% of loci under less constraint or positive selection (Figure 1), indicating that overall the genome of P. cynomolgi is highly conserved in single locus genes when compared to P. vivax, and emphasizing the value of P. cynomolgi as a biomedical and evolutionary model for studying P. vivax.
Our generation of the first P. cynomolgi genome sequences is a critical component in the development of a robust model system for the intractable and neglected P. vivax species27. Comparative genome analysis of P. vivax and the OWM malaria parasites P. cynomolgi and P. knowlesi presented here provides the foundation for further insights into traits such as host specificity that will enhance the prospects for the eventual elimination of vivax malaria and global malaria eradication.
Details of the origin of P. cynomolgi B, Berok and Cambodian strains, their growth in macaques, and isolation of parasite material are given in the Supplementary Note.
P. cynomolgi B strain was sequenced using Roche/454 GS FLX (Titanium) and Illumina/Solexa GAII platforms to 161 × coverage. In addition, 2,784 clones (6.8 Mb) of a ~40 kb insert fosmid library in pCC1FOS (Epidentre Biotechnologies, USA) were sequenced by the Sanger method. A draft assembly of strain B was constructed using a combination of automated assembly and manual gap closure. We first generated de novo contigs by assembling Roche 454 reads using GS De Novo Assembler version 2.0 with default parameters. Contigs > 500-bp were mapped to the P. vivax Salvador I reference assembly12 (PlasmoDB; see URLs). P. cynomolgi contigs were iteratively arrayed by aligning to P. vivax-assembled sequences with manual corrections. A total of 1,264 aligned contigs were validated by mapping paired-end reads from fosmid clones using BLASTN (e-value: <1e-15, identity: >90%, coverage: >200bp) implemented in the software GenomeMatcher version 1.6528. Additional linkages (699 regions) were made using PCR across the intervening sequence gaps with primers designed from neighboring contigs. Length of sequence gaps was estimated from insert lengths of the fosmid paired-end reads, the size of PCR products and homologous sequences of the P. vivax genome. Supercontigs were then manually constructed from the aligned contigs. Eventually we obtained 14 supercontigs corresponding to the 14 chromosomes of the parasite, with a total length of ~22.73 Mb, encompassing ~ 80% of the predicted P. cynomolgi genome. A total of 1,651 contigs (>1 kb) with a total length of 3.45 Mb were identified as unassigned subtelomeric sequences by searching against the P. vivax genome using BLASTN. Additionally, in order to improve sequence accuracy, we constructed a mapping assembly of Illumina paired-end reads and the 14 supercontigs and unassigned contigs as reference sequences using CLC Genomics Workbench version 3.0 with default settings (CLC Bio, Denmark). Comparison of the draft P. cynomolgi B sequence with 23 P. cynomolgi protein-coding genes (64 kb) obtained by Sanger sequencing showed 99.8 % sequence identity (Supplementary Table 13). P. cynomolgi Berok and Cambodian strains were sequenced to 26 × and 17 × coverage respectively, using the Roche/454 GS FLX (Titanium) platform, with single-end and 3 kb paired-end libraries made for the former and a single-end library only made for the latter. For phylogenetic analyses of specific genes, sequences were independently verified by Sanger sequencing (Supplementary Note and Supplementary Table 14).
Gene prediction of the 14 supercontigs and 1,651 unassigned contigs was performed using the MAKER genome annotation pipeline29 using ab initio gene prediction programs trained on protein and ESTs from PlasmoDB Build 7.1. For gene annotation, BLASTN (e-value: <1e−15, identity: >70%, coverage: >100bp) searches of P. vivax (PvivaxAnnotatedTranscripts_PlasmoDB-7.1.fasta) and P. knowlesi (PknowlesiAnnotatedTranscripts_PlasmoDB-7.1.fasta) predicted proteomes were run and the best-hits identified. All predicted genes were manually inspected at least twice for gene structure and functional annotation, and orthologous relationships between P. cynomolgi, P. vivax and P. knowlesi determined based upon synteny. A unique identifier was assigned to P. cynomolgi genes as follows: PCYB_######, where the first two of the six numbers indicate chromosome number. Paralogs of genes that appeared to be specific to either P. cynomolgi, P. vivax or P. knowlesi were searched using BLASTP with default parameters using cut-off e-value of <1e−16.
Predicted proteins of P. cynomolgi B strain were concatenated and aligned with those in the 14 chromosomes of five other Plasmodium genomes, P. vivax, P. knowlesi, P. falciparum, P. berghei and P. chabaudi, using the software Murasaki version 1.68.630.
Eleven P. cynomolgi CYIR proteins (with sequence similarity to P. knowlesi KIR) were subjected to BLASTP search for regions having high similarity to host Macacca mulatta CD99 protein, with cut-off e-value of <1e−12 and compositional adjustment (i.e., no adjustment) against the non-redundant protein sequence dataset of the M. mulatta proteome in NCBI.
Genes were aligned using Clustal W version 2.0.1031 with manual corrections, and unambiguously aligned sites were selected for phylogenetic analyses. Maximum Likelihood (ML) phylogenetic trees were constructed using PROML programs in PHYLIP version 3.6932 under Jones-Taylor-Thornton (JTT) amino acid substitution model. To take the evolutionary rate heterogeneity across sites into consideration, the R (Hidden Markov Model rates) option was set for discrete G distribution with 8 categories for approximating the site-rate distribution. CODEML programs in PAML 4.433 were used for estimating the G shape parameter, a values. For bootstrap analyses, SEQBOOT and CONSENSE programs in PHYLIP were applied.
We undertook two approaches. First, genes unique to P. vivax and P. cynomolgi (hypnozoite-forming parasites) and not found in other non-hypnozoite-forming Plasmodium species were identified. We used the 147 unique genes identified in the P. vivax genome12 to search the P. cynomolgi B sequence. The orthologs identified in both species were then searched ~1 kb 5’ upstream for four specific ApiAP2 motifs20, PF14 0633: GCATGC, PF13_0235_D1: GCCCCG, PFF0670w_D1: TAAGCC, and PFD0985w_D2: TGTTAC, which are involved in sporozoite stage-specific regulation and expression (corresponding to the pre-hypnozoite stage). Second, ‘dormancy related’ proteins were retrieved from GenBank and used to search for P. vivax homologs. Candidate genes (n= 128) and orthologs of P. cynomolgi and five other parasite species were searched in the region ~1 kb 5’ upstream for the presence of the four ApiAP2 motifs. Data of P. vivax, P. knowlesi, P. falciparum, P. berghei, P. chabaudi and P. yoelii were retrieved from PlasmoDB Build 7.1.
For SNP identification, alignment of Roche 454 data from strains B, Berok and Cambodian was performed using SSAHA234, with 0.1 mismatch rate and only unique matches reported. Potential duplicate reads generated during PCR amplification were removed, so that when multiple reads mapped at identical coordinates, only reads with the highest mapping quality were retained. We used a statistical method by Li et al.35 implemented in SAMtools version 0.1.18 to call SNPs simultaneously in the case of duplicate runs of the same strain. SNPs with high read depth (>100) were filtered out, as were SNPs in poor alignment regions at the ends of chromosomes (Supplementary Note).
Nucleotide diversity (π) was calculated as follows: for each site being compared, we calculated allele frequency by counting the two alleles and measured the proportion of nucleotide differences. Let π be the genetic distance between allele i and allele j, then the nucleotide diversity within the population is where Pi and Pj are the overall allele frequencies i and j respectively. Mean π was calculated by averaging over sites, weighting each by where n is the number of aligned sites. Average dN/dS ratios were estimated using the modified Nei-Gojobori/Jukes-Cantor method in MEGA 436.
CNV-seq23 was used to identify potential copy number variants in P. cynomolgi. Briefly, this method is based on a statistical model that allows confidence assessment of observed copy number ratios from next generation sequencing data. Roche 454 sequences from P. cynomolgi strain B assembly was used as the reference genome, and the P. cynomolgi Berok strain used as a test genome; the Cambodian strain sequence coverage was considered too low for analysis. The test reads were mapped to the reference genome, and CNVs detected by computing the number of reads for each test strain in a sliding window. The validity of the observed ratios were assessed by the computation of a probability of a random occurrence, given no copy number variation.
Polymorphic microsatellites (defined as repeat units of 1–6 nc) between P. cynomolgi strains B and Berok were identified by aligning contigs from a de novo assembly of Berok (generated using Roche GS Assembler version 2.6, with 40 bp minimum overlap, 90% identity) to the B strain using BWA37 and allowing for gaps. Utilizing the Phred-scaled probability of the base being misaligned by SAMtools35, indel candidates were called from the alignment. In-house Python scripts were used to then cross-reference with the microsatellites found in the reference strain B assembly identified by MISA (see URLs). All homopolymer microsatellites were discarded to account for potential sequence errors introduced by 454 sequencing.
Selective constraint analysis of 4,605 orthologs between P. cynomolgi strains B and Berok and P. vivax Salvador I, utilized MUSCLE38 alignments with stringent removal of gaps and missing data (P. cynomolgi Berok orthologs were identified through a reciprocal best hit BLAST search against strain B genes). Analyses were conducted using the Nei-Gojobori model25. In order to detect values that could not be explained by chance, we estimated the standard error (SE) by a bootstrap procedure with 200 pseudo-replicates for each gene. The expected value for Ds-Dn is 0 if a given pair of sequences is diverging without obvious effects on fitness. In the case of the intra-P. cynomolgi comparison, values with a difference of ±2 SE from 0 were considered indicative of an excess of synonymous changes (Ds-Dn>0) or non-synonymous changes (Ds-Dn<0). In the case of the inter-P. cynomolgi-P. vivax comparison, we used a more stringent criterion of ±3 SE from 0.
We thank Hiromi Sawai for suggestions of genome analysis, David Fisher for help with genome-wide evolutionary analyses, and NYU Langone Medical Center Genome Technology Core for access to Roche 454 sequencing equipment funded by grant S10 RR026950 to J.M.C. from the National Institutes of Health (NIH). Genome and phylogenetic analyses used the Genome Information Research Center in the Research Institute of Microbial Diseases, Osaka University. This work was supported by the Ministry of Education, Culture, Sports, Science and Technology grants (18073013, 18GS03140013, 20390120, 22406012 and 22406012) to K.T., NIH grant R01 GM07079393-01A2, Burroughs Wellcome Fund grant 1007398 and NIH International Centers of Excellence for Malaria Research grant U19 AI089676-01 to J.M.C., and NIH grant R01 GM080586 to AAE.
Accession codes. The P. cynomolgi B, Cambodian and Berok strains have been deposited in DDBJ/EMBL/GenBank databases with the following accession numbers: B strain sequence reads DRA000196, genome assembly BAEJ01000001 to BAEJ01003341, and annotation DF157093-DF158755; Cambodian strain sequence reads DRA000197; Berok strain sequence reads SRA047950.1. SNP calls have been submitted to dbSNP (handle: NYU_CGSB_BIO; batch id: 1056645). Sequences of the dbp genes from P. cynomolgi (Cambodian strain), P. fieldi (A.b.i. strain), and P. simiovale (AB617788-AB617791), and P. cynomolgi Berok strain (JQ422035-JQ422036), and rbp gene sequences from P. cynomolgi Berok and Cambodian (JQ422037-JQ422050), were deposited. The complete apicoplast genome of P. cynomolgi Berok was also deposited (JQ522954). The P. cynomolgi B reference genome is also available through PlasmoDB (see URLs).
AUTHOR CONTRIBUTIONSK.T., J.M.C., A.A.E., and J.W.B. conceived and conducted the study. S.K., Y.K., Y.Y., S.I.T. and J.W.B. provided P. cynomolgi material. S.N., N.G., T.Y. and H.R.K. constructed a computing system for data processing, and S.I.T., H.H., P.L.S, S.A.S. and H.R.K. performed scaffolding of contigs and manual annotation of the predicted genes. S.N. performed sequence correction of supercontigs and gene prediction. S.I.T., S.N., N.G., N.A., M.Y., O.K., K.T., H.R.K., R.S., S.A.S. and J.M.C. analyzed data. S.I.T. N.M.Q.P., T.T., T.M., K.K., J.M.C., T.H., A.A.E., J.W.B. and K.T. wrote the manuscript.
COMPETING FINANCIAL INTERESTS
The authors declare no competing financial interests.