The majority of known Toxoplasma gondii isolates from Europe and North America belong to three clonal lines that differ dramatically in their virulence, depending on the host. To identify the responsible genes, we mapped virulence in F1 progeny derived from crosses between type II and type III strains, which we introduced into mice. Five virulence (VIR) loci were thus identified, and for two of these, genetic complementation showed that a predicted protein kinase (ROP18 and ROP16, respectively) is the key molecule. Both are hypervariable rhoptry proteins that are secreted into the host cell upon invasion. These results suggest that secreted kinases unique to the Apicomplexa are crucial in the host-pathogen interaction.Toxoplasma gondii is an obligate intracellular parasite capable of infecting a wide variety of warm-blooded animals. Infections are widespread in humans and can lead to severe disease in utero or in individuals with a suppressed immune system. The majority of European and North American isolates belong to three distinct clonal lines, referred to as types I, II, and III (1,2). Types I and III appear to be the result of just one or two matings between an ancestral type II strain and, respectively, one or other of a pair of closely related strains that are distinct from type II (3-6). The three major Toxoplasma lines differ in a number of phenotypes (7), the best described of which is virulence in mice: type I strains are the most virulent with a lethal dose (LD 100 ) of one parasite (8,9), whereas types II and III have values for median lethal dose (LD 50 ) that range from 10 2 to 10 5 . There may also be differences in the virulence of the three strains in humans (10-12).Previously (3), we demonstrated that a cross between a type II and a type III strain produced F 1 progeny (S23 and CL11) that were more virulent (up to 3 logs) than 14 of their siblings (3). Because only two of the 16 progeny showed this difference, it was likely that multiple loci controlled virulence in these strains, and to identify these loci, we phenotyped 23 additional recombinant F 1 progeny from II × III crosses (13,14). Progeny with high virulence were identified by infecting mice with 100 tachyzoites; progeny with very low virulence were identified by infecting mice with 100,000 parasites. †To whom correspondence should be addressed.

Background: A common feature of microarray experiments is the occurence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative background-corrected intensities. The efficiency and power of an analysis performed can be substantially reduced by having an incomplete matrix of gene intensities. Additionally, most statistical methods require a complete intensity matrix. Furthermore, biases may be introduced into analyses through missing information on some genes. Thus methods for appropriately replacing (imputing) missing data and/or weighting poor quality spots are required.

The Apicomplexa is a highly diverse phylum of parasitic protists that includes the causative agents of malaria and other important human and animal diseases. These unicellular pathogens have been shaped by a key evolutionary event: the secondary endosymbiosis of a single eukaryotic cell and photosynthetic algae. From this event and subsequent evolution, most species in the phylum retain a single mitochondrion and a plastid‐like organelle known as the apicoplast ( see The organelles of Apicomplexan parasites ). The reduced function of these organelles is mirrored by their highly compact genomes, where genes have been lost or transferred to the nucleus, making the nuclear genome a mosaic of former organellar genes embedded in chromosomal DNA from both endosymbionts. Natural selection on this basic cellular and genetic plan has led to a diversity of parasitic life cycles, each with adaptations that specify host range and mechanisms of transmission. Comparative genomics is beginning to reveal the similarities and differences between member species, enhancing our capability to treat and control the devastating diseases they cause.

The apicomplexa are a highly diverse phylum of parasitic protists that are descended from a secondary endosymbiosis of a photosynthetic algae and single eukaryotic cell. Throughout the evolution of the phylum, most species have maintained a single mitochondrion and a plastid‐like organelle called the apicoplast. The genomes associated with these organelles are vastly reduced compared to counterparts in other eukaryotic lineages and this probably reflects a concomitant reduction in function.