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Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants

Irene Lindström Bontell16, Neil Hall2, Kevin E Ashelford2, JP Dubey3, Jon P Boyle4, Johan Lindh5 and Judith E Smith1*

Author Affiliations

1 Institute of Integrative and Comparative Biology, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK

2 School of Biological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK

3 United States Department of Agriculture, Agricultural Research Service, Animal and Natural Resources Institute, Animal Parasitic Diseases Laboratory, Baltimore Avenue, Beltsville, MD 20705, USA

4 Department of Biological Sciences, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA

5 Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control (SMI), Nobels väg, 171 82 Solna, Sweden

6 Current address: Division of Clinical Microbiology, Department of Medicine, Karolinska Institutet, Alfred Nobels Allé, 141 86 Stockholm, Sweden

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Genome Biology 2009, 10:R53  doi:10.1186/gb-2009-10-5-r53

Published: 20 May 2009



Toxoplasma gondii is a zoonotic parasite of global importance. In common with many protozoan parasites it has the capacity for sexual recombination, but current evidence suggests this is rarely employed. The global population structure is dominated by a small number of clonal genotypes, which exhibit biallelic variation and limited intralineage divergence. Little is known of the genotypes present in Africa despite the importance of AIDS-associated toxoplasmosis.


We here present extensive sequence analysis of eight isolates from Uganda, including the whole genome sequencing of a type II/III recombinant isolate, TgCkUg2. 454 sequencing gave 84% coverage across the approximate 61 Mb genome and over 70,000 single nucleotide polymorphisms (SNPs) were mapped against reference strains. TgCkUg2 was shown to contain entire chromosomes of either type II or type III origin, demonstrating chromosome sorting rather than intrachromosomal recombination. We mapped 1,252 novel polymorphisms and clusters of new SNPs within coding sequence implied selective pressure on a number of genes, including surface antigens and rhoptry proteins. Further sequencing of the remaining isolates, six type II and one type III strain, confirmed the presence of novel SNPs, suggesting these are local allelic variants within Ugandan type II strains. In mice, the type III isolate had parasite burdens at least 30-fold higher than type II isolates, while the recombinant strain had an intermediate burden.


Our data demonstrate that recombination between clonal lineages does occur in nature but there is nevertheless close homology between African and North American isolates. The quantity of high confidence SNP data generated in this study and the availability of the putative parental strains to this natural recombinant provide an excellent basis for future studies of the genetic divergence and of genotype-phenotype relationships.