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

Bontell, I.L., Hall, N., Ashelford, K.E., Dubey, J.P., Boyle, J.P., Lindh, J. and Smith, J.E. (2009) Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants. Genome Biology, 10. ISSN 1465-6906

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Abstract

BACKGROUND 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.

RESULTS 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.

CONCLUSIONS 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.

Item Type: Article
Copyright, Publisher and Additional Information: © 2009 Lindström Bontell et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Academic Units: The University of Leeds > Faculty of Biological Sciences (Leeds) > Institute of Integrative and Comparative Biology (Leeds)
Depositing User: Sherpa Assistant
Date Deposited: 06 May 2010 15:37
Last Modified: 08 Feb 2013 17:06
Published Version: http://dx.doi.org/10.1186/gb-2009-10-5-r53
Status: Published
Publisher: BioMed Central
Identification Number: 10.1186/gb-2009-10-5-r53
Related URLs:
URI: http://eprints.whiterose.ac.uk/id/eprint/10810

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