Résumé
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, Plasmodium 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 two 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 co-linear 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. Interestingly, two of these
genes have been identified to also be under positive selection in the
other main human malaria agent, Plasmodium falciparum, thus suggesting
their key role in the evolution of the ability of these parasites to
infect humans or their anthropophilic vectors. We finally 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).