Abstract
BackgroundRodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the rodent malaria parasites is Plasmodium yoelii, and multiple P. yoelii strains or subspecies that cause different disease phenotypes have been widely employed in various studies. The genomes and transcriptomes of several P. yoelii strains have been analyzed and annotated, including the lethal strains of P. y. yoelii YM (or 17XL) and non-lethal strains of P. y. yoelii 17XNL/17X. Genomic DNA sequences and cDNA reads from another subspecies P. y. nigeriensis N67 have been reported for studies of genetic polymorphisms and parasite response to drugs, but its genome has not been assembled and annotated.ResultsWe performed genome sequencing of the N67 parasite using the PacBio long-read sequencing technology, de novo assembled its genome and transcriptome, and predicted 5383 genes with high overall annotation quality. Comparison of the annotated genome of the N67 parasite with those of YM and 17X parasites revealed a set of genes with N67-specific orthology, expansion of gene families, particularly the homologs of the Plasmodium chabaudi erythrocyte membrane antigen, large numbers of SNPs and indels, and proteins predicted to interact with host immune responses based on their functional domains.ConclusionsThe genomes of N67 and 17X parasites are highly diverse, having approximately one polymorphic site per 50 base pairs of DNA. The annotated N67 genome and transcriptome provide searchable databases for fast retrieval of genes and proteins, which will greatly facilitate our efforts in studying the parasite biology and gene function and in developing effective control measures against malaria.
Highlights
Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development
Gene families from three P. yoelii parasites Among the predicted genes and proteins, we identified 22 gene families that have been previously found in Plasmodium yoelii [36] with at least one member detected in Plasmodium y. nigeriensis N67 (N67) (Table S10)
Illumina-based RNA and DNA sequencing of the N67 parasite have been performed for studying genetic polymorphisms and parasite response to drugs [6, 20], assembly of the N67 genome and prediction of gene functions have not been reported previously due to difficulties in assembling AT-rich short sequence reads
Summary
Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. Some of the P. yoelii strains are genetically diverse, whereas others are closely related or derived from a common ancestor during laboratory passages in mice [4, 6, 7] Mice infected with these P. yoelii strains generally have dramatic differences in parasitemia, disease severity, pathology, and host immune response [8]. These parasites stimulate different host responses and pathology [9,10,11,12]. Identification of the genes or genetic differences between N67 and N67C parasite will facilitate our understanding of the molecular mechanisms of virulence and disease phenotypes in these infections
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