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Project summary

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.  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 and its goal is 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.  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 trough 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 J. Craig Venter Institute. 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 Drs. Omoto and 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.

Updates

  • Hammondia hammondi genomic sequence has been submitted to GenBank The new assembly for the H. hammondia genome has benn submitted to GenBank. The accession number is AHJH00000000.
    Posted Apr 5, 2012, 3:06 PM by Hernan Lorenzi
  • GenBank submission of T. gondii TgCatBr5 and RUB strains are done. Toxoplasma gondii RUB and TgCatBr5 strains have been deposited in GenBank. Assembly accessions are:Toxoplasma gondii RUB    AFYV00000000 Toxoplasma gondii TgCatBr5 AFPV00000000
    Posted Aug 31, 2011, 10:43 AM by Hernan Lorenzi
  • The Gregarina niphandrodes genome has been released in GenBank A draft version of the G. niphandrodes genomes has been release at GenBank with Accession Number AFNH00000000
    Posted Jun 28, 2011, 5:43 PM by Hernan Lorenzi
  • Approved revision of the current T. gondii GSCID project A revision to the current T. gondii GSCID project has been approved by the NIAID. The proposed changes are the following: 1)    Substitution of 5 isolates of similar genotype, where ...
    Posted May 18, 2011, 11:29 AM by Hernan Lorenzi
  • Toxoplasma gondii TgCatBr9 assembly has been released at GenBank The assembly of T. gondii TgCatBr9 strain has been released to GenBank. The GenBank information is posted below.  PID     Organism                       Accession---------------------------------------------------61549    Toxoplasma gondii TgCATBr9    AFHV00000000
    Posted May 18, 2011, 11:13 AM by Hernan Lorenzi
Showing posts 1 - 5 of 13. View more »

Coming up...

OwnerDescriptionDue DateComplete
Hernan Lorenzi GenBank submission of T. gondii VAND assembly  February 28, 2011  
Hernan Lorenzi GenBank submission of T. gondii p89 assembly February 28, 2011  
Hernan Lorenzi GenBank submission of T. gondii FOU assembly February 28, 2011  
Hernan Lorenzi GenBank submission T. gondii MAS assembly February 28, 2011  
Hernan Lorenzi Final assembly for TgCatBr9 strain March 31, 2011  
Hernan Lorenzi GenBank submission of G. niphandrodes assembly May 31, 2011  
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