Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

Gilabert, A. et al. (2018) Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution. PLoS Biology, 16(8), e2006035. (doi: 10.1371/journal.pbio.2006035) (PMID:30142149)

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Abstract

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]).

Item Type:Articles
Additional Information: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: modaliteÂs des transferts inter- espèces 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.
Keywords:Methods and resources, biology and life sciences, computer and information sciences, medicine and health sciences, research and analysis methods
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Creator Roles:
Otto, T. D.Conceptualization, Data curation, Formal analysis, Writing – original draft, Writing – review and editing
Authors: Gilabert, A., Otto, T. D., Rutledge, G. G., Franzon, B., Ollomo, B., Arnathau, C., Durand, P., Moukodoum, N. D., Okouga, A.-P., Ngoubangoye, B., Makanga, B., Boundenga, L., Paupy, C., Renaud, F., Prugnolle, F., and Rougeron, V.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:PLoS Biology
Publisher:Public Library of Science
ISSN:1544-9173
ISSN (Online):1545-7885
Copyright Holders:Copyright © 2018 The Authors
First Published:First published in PLoS Biology 16(8):e2006035
Publisher Policy:Reproduced under a Creative Commons License

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