Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, P. vivax-like, was discovered in African great apes and is hypothesized to have given rise to P. vivax in humans. To unravel the evolutionary history and adaptation of P. vivax to different host environments, we generated using long- and short-read sequence technologies 2 new P. vivax-like reference genomes and 9 additional P. vivax-like genotypes. Analyses show that the genomes of P. vivax and P. vivax-like are highly similar and colinear within the core regions. Phylogenetic analyses clearly show that P. vivax-like parasites form a genetically distinct clade from P. vivax. Concerning the relative divergence dating, we show that the evolution of P. vivax in humans did not occur at the same time as the other agents of human malaria, thus suggesting that the transfer of Plasmodium parasites to humans happened several times independently over the history of the Homo genus. We further identify several key genes that exhibit signatures of positive selection exclusively in the human P. vivax parasites. Two of these genes have been identified to also be under positive selection in the other main human malaria agent, P. falciparum, thus suggesting their key role in the evolution of the ability of these parasites to infect humans or their anthropophilic vectors. Finally, we demonstrate that some gene families important for red blood cell (RBC) invasion (a key step of the life cycle of these parasites) have undergone lineage-specific evolution in the human parasite (e.g., reticulocyte-binding proteins [RBPs]).
Fig. 1 rbp genes in P. vivax-like and P. vivax. Maximum likelihood phylogenetic tree of all full-length rbp genes in P. vivax-like Pvl01 (in blue), P. vivax SalI and PvP01 strains (in green), P. cynomolgi B strain, and P. knowlesi H strain (in black). Bootstrap values, calculated by RAxML bootstrapping posterior probability, are indicated. The different subclasses of rbp are indicated as rbp1, rbp2, and rbp3. The black stars indicate pseudogenes. The animal pictograms indicate the primate host.
Fig. 2 Relative divergence dating between P. vivax and P. vivax-like. Maximum likelihood phylogenetic tree of 13 Plasmodium species, including P. vivax and P. vivax-like. The analysis was based on an alignment of 2,784 one-to-one orthologous groups across the 13 Plasmodium reference genomes (see Materials and methods section). Values indicated at the nodes are the 95% CIs of the relative splits estimated using the method developed by Silva and colleagues  (values in blue) and the RelTime method  (values in red; ×100). Results are given for the analyses performed considering the JTT model of evolution. For the Silva method , we gave for the internal nodes the minimal and maximal values of the lower and upper limits of the 95% CI of all possible pairwise species combinations. The table gives the ratio between the relative divergence times of the human–nonhuman Plasmodium species pairs. The final alignment of the 2,784 one-to-one orthologues—excluding ambiguities, lox-complexity regions, and poorly aligned regions—and the tree are available as supplemental files in S3 Data. CI, confidence interval; JTT, Jones, Taylor, and Thornton; Pf, P. falciparum; Pkn, P. knowlesi; Pm, P. malariae; Pml, P. malariae-like; Poc, P. ovale curtisi; Pow, P. ovale wallikeri; Pprf, P. praefalciparum; Pv, P. vivax; Pvl, P. vivax-like.
Fig. 3 ML phylogenetic tree with 1,000 bootstraps computed by alignment to the P. cynomolgi B strain genome, based on 100,616 SNVs shared by 11 P. vivax-like and 19 P. vivax samples. A position was considered an SNV if at least one sample carried a different nucleotide compared with the PvP01 reference. No missing data were allowed, and a minimum depth of 5 reads per position was considered. To overcome issues relating to multiple infections, we considered the dominant infection only by selecting the dominant allele (see Materials and methods for details). Bootstrap values superior to 70% are indicated. The host in which the Plasmodium parasite was detected is indicated by the pictograms (human, chimpanzee, and An. moucheti). This phylogeny showed the presence of a significantly distinct clade (high bootstrap values associated with each clade) composed of P. vivax-like strains on one side (light blue) and human P. vivax isolates on the other side (light green). Data (the alignment and the tree file obtained by the ML phylogenetic analysis) can be found in S5 Data. ML, maximum likelihood; SNV, single nucleotide variant.
- Aude Gilabert, Thomas D. Otto, Gavin G. Rutledge, Blaise Franzon, Benjamin Ollomo, Celine Arnathau, Patrick Durand, Nancy D. Moukodoum, Alain Prince Okouga, Barthelemy Ngoubangoye, Boris Makanga, Larson Boundenga, Christophe Paupy, Francois Renaud, Franck Prugnolle, Virginie Rougeron
- firstname.lastname@example.org - email@example.com
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom - Institute of Infection, Immunity and Inflammation, University of Glasgow, College of Medical, Veterinary and Life Sciences, Glasgow, United Kingdom - Centre International de Recherches Medicales de Franceville, Franceville, Gabon
- Agence Nationale de la Recherche Jeunes Chercheurs Jeunes Chercheuses http://www. agence-nationale-recherche.fr/Project-ANR-12- JSV7-0006 (grant number ORIGIN Origin, adaptation and evolution of Plasmodium falciparum). Received by FP. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Agence Nationale de la Recherche Tremplin-ERC (TERC3) 2017 http://www.agence- nationale-recherche.fr/Project-ANR-17-ERC3-0002 (grant number EVAD: Evolutionary history and genetic adaptation of Plasmodium vivax). Received by VR. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Laboratoire Mixte International https://www.ird.fr/infos-pratiques/ archives/anciens-lmi/lmi-zofac-zoonoses-dans-les- forets-tropicales-humides-d-afrique-centrale- modalites-des-transferts-inter-especes-et- adaptation-des-pathogenes (grant number ZOFAC: zoonoses dans les forêts tropicales humides d’Afrique centrale: modalite´s des transferts interespèces et adaptation des pathogènes). Received by FP. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Medical Research Council Doctoral Training Grant (grant number MR/J004111/1). Received by GGR. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Wellcome Trust https://www. genomethics.org/overview.html (grant number 098051 Genome Ethics). Received by GGR. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
PLoS Biol. 16, e2006035 (2018)