Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

By J. Carlton, Samuel V. Angiuoli, Bernard B. Suh, Taco W. A. Kooij, Mihaela Pertea, Joana C. Silva, Maria D. Ermolaeva, Jonathan E. Allen, Jeremy D. Selengut, H. Koo and 34 more. Nature, 2002

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Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.

Subfields: Immunology, Molecular Biology, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/3dde9bed650303ebdbb5c182f0227a71c968c53b

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Citations in the corpus

Tropical infectious diseases: Metabolic maps and functions of the Plasmodium falciparum apicoplast (2004, background): “This protein is not recognized by automated tools like other apicoplast-targeted proteins, but still has an 80 amino-acid amino-terminal extension, which contains a signal peptide followed by a region of positively charged amino acids — similar to the Plasmodium yoelii homologu”
Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences (2003, neutral): “ [111] Dictyostelium discoideum 0.437 11000 32000000 Calculations based on analysis of chromosome 2. [112] Plasmodium falciparum 0.474 5268 22853764 [113] Plasmodium yoelii yoelii 0.494 5878 23100000 [114] Trypanosoma brucei** 0.52 687 2258403 Calculations based on chromomsomes I and II (~10% of the”
OrthoMCL: identification of ortholog groups for eukaryotic genomes. (2003, background): “2), minimizing errors attributable to missing genes, because diverged paralogs are likely to exhibit lower similarity to each other when compared with the similarities between true orthologs.”
A review of methods and databases for metagenomic classification and assembly (2019, background): “A major advantage of rRNA analysis is that databases such as Greengenes [10], RDP [11] and SILVA [12] contain genes from millions of species, making them far more comprehensive than genome databases, which contain tens of thousands of species.”
Comparative Genomics in Eukaryotes (2005, background): “…divergance between the rodent parasite Plasmodium y. yoelii and the human parasite P. falciparum is approximately the same as that between human and mouse (Carlton et al., 2002), leading to the expectation that cis-regulatory elements will also be conserved between these two Plasmodium species.”
Versatile and open software for comparing large genomes (2004, result): “More distantly related pairs of species, for example, Plasmodium falciparum and P. yoelii , fail to show DNA sequence similarity but do show large-scale similarity when their translated protein sequences are aligned, as described in earlier studies [7,8].”