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Background  The phylum Apicomplexa comprises important unicellular human parasites such as  Toxoplasma  and  Plasmodium. Eimeria  is the largest and most diverse genus of apicomplexan parasites and some species of the genus are the causative agent of coccidiosis, a disease economically devastating in poultry. We report a complete genome sequence of the mouse parasite  Eimeria falciformis . We assembled and annotated the genome sequence to study host-parasite interactions in this understudied genus in a model organism host.    Results  The genome of  E. falciformis  is 44 Mb in size and contains 5,879 predicted protein coding genes. Comparative analysis of  E. falciformis  with  Toxoplasma gondii  shows an emergence and diversification of gene families associated with motility and invasion mainly at the level of the Coccidia. Many rhoptry kinases, among them important virulence factors in  T. gondii , are absent from the  E. falciformis  genome. Surface antigens are divergent between Eimeria species. Comparisons with  T. gondii  showed differences between genes involved in metabolism, N-glycan and GPI-anchor synthesis.  E. falciformis  possesses a reduced set of transmembrane transporters and we suggest an altered mode of iron uptake in the genus  Eimeria .    Conclusions  Reduced diversity of genes required for host-parasite interaction and transmembrane transport allow hypotheses on host adaptation and specialization of a single host parasite. The  E. falciformis  genome sequence sheds light on the evolution of the Coccidia and helps to identify determinants of host-parasite interaction critical for drug and vaccine development.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-696) contains supplementary material, which is available to authorized users.

The genome of Eimeria falciformis - reduction and specialization in a single host apicomplexan parasite