Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species

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Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species
Bardil, Amélie; Berthomieu, Arnaud; Dainat, Jacques; Fontaine, Michael; Hellgren, Olof; Rivero, Ana; Otto, Thomas; Gandon, Sylvain, 2026, "Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species", https://doi.org/10.23708/0QPMON, DataSuds, V1
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Description
Data and script supporting the paper: "The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species."

Avian malaria parasites form a highly prevalent and genetically diverse group within the haemosporidians, yet they have long been overlooked relative to their human- and rodent-infecting counterparts. Among these, parasites of the genus Haemoproteus (Haemosporida, Haemoproteidae) are widespread and prevalent blood parasites of birds, transmitted by louse flies (Hippoboscidae) and biting midges (Ceratopogonidae). Recent phylogenomic analyses place Haemoproteus parasites at the root of the haemosporidian tree, making genomic data from these taxa essential for understanding the evolutionary origins of malaria parasites. To date, only two avian Plasmodium and one avian Haemoproteus genomes have been sequenced. We present the first assembled genome of Haemoproteus majoris (lineage WW2), a common blood parasite of passerine birds. As avian erythrocytes are nucleated, parasite DNA was enriched by FACS-based sorting to discriminate and isolate the parasite from host cell nuclei prior to whole-genome amplification. The genome was assembled using Nanopore long-read sequencing and polished with Illumina short-reads, yielding 145 contigs with a total assembly size of 23.9Mb and a G+C content of 27.85%. Genome annotation identified 5501 protein-coding genes, 69 non-coding RNA genes, and 57 long terminal repeat retrotransposons (LRT-RTs), including one full-length element. This archive provides the genomic resources in their original format before being processed by EBI-ENA.

This archive includes:
  • 1. the reference assembly as generated in the paper; The assembly was also uploaded to the ENA under the accession no.: GCA_965637345.1.
  • 2. The original genome annotation in GFF format (not processed by the ENA),
  • 3. A compressed archive of the GitHub which provides all the bioinformatic details of the scripts used to generate the genome and its annotation. The original is available here: https://github.com/mikafontaine/malaria_HaemoproteusWW2.
(2026-06-30)
Subject Agricultural Sciences; Earth and Environmental Sciences; Medicine, Health and Life Sciences
Keyword Malaria, Avian, Haemoproteus majoris, Genome, genome annotation, parasite, Plasmodium
Related Publication Amélie Bardil, Arnaud Berthomieu, Jacques Dainat, Michael C. Fontaine, Olof Hellgren, Ana Rivero, Thomas D. Otto, Sylvain Gandon (2026). The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species. bioRxiv 2026.07.13.738139 doi: 10.64898/2026.07.13.738139
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malaria_HaemoproteusWW2_githubarchive.tar.gz
Gzip Archive - 1.3 MB
Published Aug 5, 2026
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MD5: 05f79c3754ecdb187aa28d5caf9cc54f
Compressed archive of the GitHub which provides all the bioinformatic details of the scripts used to generate the genome and its annotation. The original is available here: https://github.com/mikafontaine/malaria_HaemoproteusWW2.
CodeDocumentation
ReadMe_DOI_10_23708_0QPMON.txt
Plain Text - 2.6 KB
Published Aug 5, 2026
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MD5: 8dc0b5a6fe090c38c1feb4183cd0149d
contains the citation, description and conditions of use, or even access, depending on the case, to the dataset
Documentation
Preview "ReadMe_DOI_10_23708_0QPMON.txt"
WW2.ILRA.fasta.gz
WW2/Gzip Archive - 6.3 MB
Published Aug 5, 2026
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MD5: 538f59792015594f54fffeabac1bafd7
Original genome assembly for Haemoproteus majoris (lineage WW2). The genome was assembled using Nanopore long-read sequencing and polished with Illumina short-reads, yielding 145 contigs with a total assembly size of 23.9Mb and a G+C content of 27.85%. More details are provided in the manuscript and the associated GitHub repository (https://github.com/mikafontaine/malaria_HaemoproteusWW2).
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WW2_hardmaskup.gff3.gz
WW2/Gzip Archive - 749.1 KB
Published Aug 5, 2026
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MD5: 3f41fe888c5a06d338be77d8245db71e
Genome annotations associated with the WW2 reference assembly. The genome annotation was generated using the tool Companion (v2.2.11, Release 63) (Haese-Hill W, Crouch K, Otto TD. 2024, https://doi.org/10.1093/nar/gkae378). More details are provided in the manuscript and the associated GitHub repository (https://github.com/mikafontaine/malaria_HaemoproteusWW2).
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