Replication Data for: Identification of two genomic cryptotypes of Plasmodium malariae in Africa

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Replication Data for: Identification of two genomic cryptotypes of Plasmodium malariae in Africa
Lefebvre, Margaux; Arnathau, Céline; Houzé, Sandrine; De Thoisy, Benoit; González, Camila; Rondón, Silvia; Pain, Arnab; Fontaine, Michael C.; Prugnolle, Franck; Rougeron, Virginie, 2026, "Replication Data for: Identification of two genomic cryptotypes of Plasmodium malariae in Africa", https://doi.org/10.23708/PXTDVF, DataSuds, V1
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Description
These data and scripts are accompanying the manuscript: "Identification of two genomic cryptotypes of Plasmodium malariae in Africa" by Margaux J. M. Lefebvre*, Céline Arnathau, Sandrine Houzé, Benoit de Thoisy, Camila González, Silvia Rondón, Arnab Pain, Michael C. Fontaine§*, Franck Prugnolle§* & Virginie Rougeron§* (*, contact person; § co-supervisors and co-last authors). The archive here includes:
  • malariae_brasi.filt.core.ploidy2.vcf.gz: the SNP polymorphism data in VCF format.
  • Scripts_WGSPmalariae.tar all the scripts and explanations that are provided in the GitHub repository accompanying the manuscript (https://github.com/MargauxLefebvre/WGS_Pmalariae.git) in a zipped folder.
  • README.txt: additional explanations related to the data.
Context and scientific goals: Plasmodium malariae is a human malaria parasite widely distributed across Africa, yet its population structure and genomic diversity remain incompletely characterized because of limited whole-genome data from the continent. In addition, the evolutionary and genetic relationships between P. malariae and the closely related simian parasite from South America, Plasmodium brasilianum, are still not fully understood due to the scarcity of genomic resources. To address these knowledge gaps, this study analyzed parasite genomes obtained from infected humans and non-human primates to investigate genetic diversity, population structure, and signatures of adaptation. Specifically, the objectives were to expand and strengthen the African whole-genome dataset for P. malariae and to generate additional genomic data for P. brasilianum, thereby improving our understanding of their genetic relationships and evolutionary history. See the manuscript for further details.
Subject Earth and Environmental Sciences; Medicine, Health and Life Sciences
Keyword Plasmodium malariae, Plasmodium brasilianum, Genetics, Population, malaria, Adaptation, Biological
Related Publication preprint article : Identification of two genomic cryptotypes of Plasmodium malariae in Africa Margaux J. M. Lefebvre, Céline Arnathau, Sandrine Houzé, Benoit de Thoisy, Camila González, Silvia Rondón, Andrés Link, Arnab Pain, Michael C. Fontaine, Franck Prugnolle, Virginie Rougeron bioRxiv 2026.03.23.713578; doi: 10.64898/2026.03.23.713578
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ReadMe_DOI_10_23708_PXTDVF.txt
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Published Jun 15, 2026
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MD5: 194c1aeb20db600322f2245d81d925f9
contains the citation, description and conditions of use, or even access, depending on the case, to the dataset
Documentation
Preview "ReadMe_DOI_10_23708_PXTDVF.txt"
malariae_brasi.filt.core.ploidy2.vcf.gz
dataset_files/Gzip Archive - 76.3 MB
Published Jun 15, 2026
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MD5: 7b5da449eb825afa0d6f7c707bf7df6a
SNP polymorphism data in VCF format. It includes only filtered SNP to include only core genomic regions and bi-allelic SNPs. See the manuscript for details.
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README.txt
dataset_files/Plain Text - 474 B
Published Jun 15, 2026
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MD5: d48873619bfe049d0d39272e992db727
README file describing the files included in this dataset
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Scripts_WGSPmalariae.tar.gzip
dataset_files/Gzip Archive - 15.4 KB
Published Jun 15, 2026
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MD5: 9f191ad7dfbc9f78479d504f3afd925c
Analysis scripts in a tar archive format. It includes all the scripts used for data analyses: available in the "Scripts_WGSPmalariae" archive, corresponding to the GitHub repository: https://github.com/MargauxLefebvre/WGS_Pmalariae.git
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