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Background   Cyclospora cayetanensis  is an apicomplexan that causes diarrhea in humans. The investigation of foodborne outbreaks of cyclosporiasis has been hampered by a lack of genetic data and poor understanding of pathogen biology. In this study we sequenced the genome of  C. cayetanensis  and inferred its metabolism and invasion components based on comparative genomic analysis.    Results  The genome organization, metabolic capabilities and potential invasion mechanism of  C. cayetanensis  are very similar to those of  Eimeria tenella . Propanoyl-CoA degradation, GPI anchor biosynthesis, and  N -glycosylation are some apparent metabolic differences between  C. cayetanensis  and  E. tenella . Unlike  Eimeria  spp., there are no active LTR-retrotransposons identified in  C. cayetanensis . The similar repertoire of host cell invasion-related proteins possessed by all coccidia suggests that  C. cayetanensis  has an invasion process similar to the one in  T. gondii  and  E. tenella . However, the significant reduction in the number of identifiable rhoptry protein kinases, phosphatases and serine protease inhibitors indicates that monoxenous coccidia, especially  C. cayetanensis,  have limited capabilities or use a different system to regulate host cell nuclear activities.  C. cayetanensis  does not possess any cluster of genes encoding the TA4-type SAG surface antigens seen in  E. tenella , and may use a different family of surface antigens in initial host cell interactions.    Conclusions  Our findings indicate that  C. cayetanensis  possesses coccidia-like metabolism and invasion components but unique surface antigens. Amino acid metabolism and post-translation modifications of proteins are some major differences between  C. cayetanensis  and other apicomplexans. The whole genome sequence data of  C. cayetanensis  improve our understanding of the biology and evolution of this major foodborne pathogen and facilitate the development of intervention measures and advanced diagnostic tools.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2632-3) contains supplementary material, which is available to authorized users.

Comparative genomics reveals Cyclospora cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens