Comparative genomic analysis of five Eimeria spp. in rabbits provides insights into coccidian tissue tropism

<i>Eimeria</i> spp. are common coccidian parasites of a wide range of vertebrates, causing diarrhoea, poor weight gain and significant mortality in domestic animals and birds. However, there is a paucity of genomic data on these important pathogens. Of the 11 common <i>Eimeria</i> species in rabbits, only <i>Eimeria stiedae</i> invades biliary epithelial cells rather than the intestine, and the determinants of coccidian tissue tropism remain unclear. In this study, we sequenced the genomes of five common rabbit <i>Eimeria</i> species, including <i>E. stiedae</i>, <i>Eimeria flavescens</i>, <i>Eimeria intestinalis</i>, <i>Eimeria magna</i> and <i>Eimeria media</i>. Comparative genomic analysis reveals that the genome of <i>E. stiedae</i> appears more compact than the genomes of intestinal <i>Eimeria</i> species. It shows reductions in the numbers of rhoptry proteins, dense granule proteins, microneme adhesive repeats and TA4 surface antigens, suggesting that surface and invasion-associated proteins may be involved in the tissue tropism of <i>Eimeria</i> spp. In addition, <i>E. stiedae</i>-specific motifs are identified in a cluster of hypothetical surface antigens. These data provide not only new insights into the biological characteristics of coccidia but also valuable resources for functional research and drug and vaccine development.