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Title: Whole genome sequencing of a recombinant type II/III Toxoplasma gondii strain from Uganda reveals chromosome sorting and local allelic variants.

item BONTELL, IRENE - University Of Leeds
item HALL, NEIL - University Of Liverpool
item ASHELFORD, KEVIN - University Of Liverpool
item Dubey, Jitender
item BOYLE, JON - University Of Pittsburgh
item LINDH, JOHAN - Swedish Institute For Infectious Disease Control
item SMITH, JUDITY - University Of Leeds

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/5/2009
Publication Date: 8/1/2009
Citation: Bontell, I.L., Hall, N., Ashelford, K.E., Dubey, J.P., Boyle, J.P., Lindh, J., Smith, J.E. 2009. Whole genome sequencing of a recombinant type II/III Toxoplasma gondii strain from Uganda reveals chromosome sorting and local allelic variants. Genome Biology 10:R53.

Interpretive Summary: Toxoplasma gondii is a single-celled parasite of all warm-blooded hosts worldwide. It causes mental retardation and loss of vision in children, and abortion in livestock. Cats are the main reservoir of T. gondii because they are the only hosts that can excrete the resistant stage (oocyst) of the parasite in the feces. Humans become infected by eating undercooked meat from infected animals and food and water contaminated with oocysts. This paper reports genetic characteristics of Toxoplasma isolates from chickens from Uganda. The results will be of interest to biologists, parasitologists, and veterinarians.

Technical Abstract: 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 >61Mb genome and over 70,000 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. 1252 novel polymorphisms were mapped and clusters of new SNPs within coding sequence implied positive selection 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. 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.