A comprehensive evaluation of rodent malaria parasite genomes and gene expression

Abstract

BackgroundRodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function.ResultsWe have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilised it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the ‘Plasmodium interspersed repeat genes’ (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family.ConclusionsComplete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-014-0086-0) contains supplementary material, which is available to authorized users.

Systematic CRISPR-Cas9-Mediated Modifications of Plasmodium yoelii ApiAP2 Genes Reveal Functional Insights into Parasite Development

“…Further investigations are necessary to dissect the functional roles of these genes, including tagging the genes for protein expression analysis. Transcriptome analysis of P. berghei showed constitutive expression of these genes in the blood stages, suggesting that they play important roles in parasite development (23).…”

“…Parasites without Pbap2-o2 had greatly reduced ookinete numbers (9), whereas Pyap2-o2-deficient and WT parasites had similar ookinete conversion rates. P. yoelii and P. berghei are closely related parasites, and approximately 90% of the predicted proteins in rodent malaria parasites (P. berghei, P. yoelii, and Plasmodium chabaudi) have orthologs in primate malaria parasites (23,29,30), supporting evolutionarily conserved gene functions in Plasmodium species. However, there are also large differences in gene families and in gene expression; for example, whole-transcriptome shotgun sequencing (RNA-seq) analyses showed only approximately 65% correlation in blood stage gene expression between P. berghei and P. yoelii (23).…”

Maternally supplied S-acyl-transferase is required for crystalloid organelle formation and transmission of the malaria parasite

“…Of 11 annotated P. berghei DHHC-PATs (17, 23) we have identified dhhc10, along with dhhc2 and dhhc3, as being up-regulated in gametocytes (Fig. 1A) (24). Whereas dhhc2 (18) and dhhc3 expression was also evident in asexual blood stage forms, only dhhc10 was exclusively transcribed in sexual stages (Fig.…”

Towards genome-wide experimental genetics in thein vivomalaria model parasitePlasmodium berghei

“…The first is the construction of the thousands of transfection constructs needed to target the *5000 genes. 15 Some advances have been made to facilitate the transfection vector construction. PCR-based construction of replacement vectors can be scaled relatively easily, but is limited to small constructs.…”

“…The availability of many complete or near-complete genome sequences [10][11][12][13][14][15] has been another huge advance towards a more profound understanding of Plasmodium biology. Genome sequence data have been a key to the scope and success of experimental genetics approaches in malaria research.…”