Data from: 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, 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). S1FigData_PvlkRAFdataset_1 samples Pvl01 to Pvl06This archive contains the vcf files listing all the high quality positions kept to draw the reference allele frequency distribution for samples Pvl01 to Pvl06. Please see the Materials and methods section for a detailed description.S1FigData_PvlkRAFdataset_1.zipS1FigData_PvlkRAFdataset_2 samples Pvl07 to Pvl09This archive contains the vcf files listing all the high quality positions kept to draw the reference allele frequency distribution for samples Pvl07 to Pvl09. Please see the Materials and methods section for a detailed description.S1FigData_PvlkRAFdataset_2.zipS1FigData_PvlkRAFdataset_3 samples Pvl10 and Pvl11This archive contains the vcf files listing all the high quality positions kept to draw the reference allele frequency distribution for samples Pvl10 and Pvl11. Please see the Materials and methods section for a detailed description.S1FigData_PvlkRAFdataset_3.zipPvivaxlikeGenomes.tarThe Pvl_genomeData folder contains the data of two genomes of Plasmodium vivax-like parasites (Pvl01 and Pvl06). Further information is included in the README within "PvivaxlikeGenomes.tar.gz"