Genome Sequencing of Clinically Important Strains of Toxoplasma Gondii

Toxoplasma gondii is a wide spread protozoan parasite of animals and an important opportunistic pathogen in humans where it causes disease in congenitally infected infants and in immunocompromised individuals. Toxoplasmosis has been implicated as the third most common source of food borne infection in the USA. Due to the risk of food and water borne infection, T. gondii is listed as a category B Biodefense Agent by NIAID. In addition to being an important pathogen, T. gondii has emerged as a model for other less tractable apicomplexan parasites. Whole genome sequences have previously been generated for three prototypic strains, (ME49, GT1 and VEG) presenting the major clonal lineages found in North America and Europe. More recent studies have detected additional genetic variation in North America and Europe, suggesting a more complex population structure than previously thought. Additionally, sampling from South America has revealed that strains from this region are highly divergent and comprise novel groups with both clonal and nonclonal genotypes. More importantly, some of these South American lineages have been associated with severe ocular disease, suggesting that differences in clinical severity may be influenced by the parasite genotype. Comparison of more than 900 strains analyzed to date indicates that they can be grouped into 14 major lineages. Current whole genome sequences are available for only 3 of these, reflecting relatively narrow genetic and biological diversity.

The Toxoplasma gondii GSCID project was funded by the NIAID in January 2010 with a goal to generate high-coverage, whole genome sequences for 13 new prototypic strains, thus providing annotated genomes for designated references strains for all 15 of the major lineages described to date. In addition, RNAseq sequencing from these same prototypic strains will be used to improve gene models. These reference strains will also be deposited into a public archive, BEI, making them available for study by the community. Besides new reference strains, the project contemplates the generation of additional 454 sequences for the ME49 strain and Illumina reads for strains GT1 and VEG to improve the quality of current assemblies. In addition, the project will generate and sequence the ends of 10,000 clones of a pToxoSuperCos cosmid genomic library of the T. gondii ME49 strain that will be made available to the community through BEI and Dr. Sibley’s Laboratory. As well, moderate-coverage, whole genome sequences will be generated for an additional 47 members of the 15 lineages to assess genetic diversity, determine population structure, and establish patterns of antigenic and allelic variation. For comparative genome analysis, we plan to sequence the genomes of two T. gondii related organisms, Gregarina niphandrodes and Hammondia hammondi. Sequencing, assembly, annotation and submissions will be carried out by the JCVI informatics staff. The required gDNA and mRNA for all T. gondii strains contemplated in this project will be provided by Dr. Sibley’s lab. Genomic DNA for G. niphandrodes and H. hammondi will be provided by Dr.Omoto and Dr.Su, respectively. Collectively these studies will foster future studies on population structure, genetic diversity, basic cellular and molecular biology of T. gondii. They are also expected to advance efforts to improve diagnostics, advance epidemiological studies, and develop new treatments to combat infection.

White Paper Access

The initial white paper submitted can be downloaded here. Since white papers are not always approved exactly as submitted, this document may not exactly describe the final form of the project. Please contact if you have any questions


Nature communications. 2016-01-07; 7.10147.
Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes
Lorenzi H, Khan A, Behnke MS, Namasivayam S, Swapna LS, Hadjithomas M, Karamycheva S, Pinney D, Brunk BP, Ajioka JW, Ajzenberg D, Boothroyd JC, Boyle JP, Dardé ML, Diaz-Miranda MA, Dubey JP, Fritz HM, Gennari SM, Gregory BD, Kim K, Saeij JP, Su C, White MW, Zhu XQ, Howe DK, Rosenthal BM, Grigg ME, Parkinson J, Liu L, Kissinger JC, Roos DS, Sibley LD
PMID: 26738725
BMC genomics. 2014-12-23; 15.1168.
NextGen sequencing reveals short double crossovers contribute disproportionately to genetic diversity in Toxoplasma gondii
Khan A, Shaik JS, Behnke M, Wang Q, Dubey JP, Lorenzi HA, Ajioka JW, Rosenthal BM, Sibley LD
PMID: 25532601


This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under contract numbers N01-AI30071 
and/or HHSN272200900007C.