Toxoplasma gondii is a zoonotic parasite from the phylum Apicomplexa. It occurs worldwide and the current estimate of human infection is 30%. Whilst human infection with T. gondii is mostly asymptomatic, it can cause severe morbidity and mortality in immunocompromised individuals. Women getting infected during pregnancy risk abortion, and their new-born may suffer from severe disease such as ocular toxoplasmosis or mental retardation. Toxoplasmosis is also an important cause of abortion in sheep and results in considerable economic losses.</p><p>T. gondii is able to infect a wide range of warm-blooded vertebrates as intermediate hosts whilst only felids serve as definitive hosts. We had used the type II strain CZ for two transcriptomic studies of the cat enteroepithelial stages of T. gondii. CZ was first isolated from the faeces of a Siberian tiger at the Dvur Králové Zoo (Czech Republic) and then cloned by limiting dilution to yield clone H3. In this study, CZ clone H3 was subjected to whole genome sequencing using Illumina technology.